Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:
URI: https://w3id.org/nmdc/nmdc
"},{"location":"#classes","title":"Classes","text":"Class Description Activity a provence-generating activity WorkflowExecutionActivity Represents an instance of an execution of a particular workflow MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysisActivity MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis MetaproteomicsAnalysisActivity MetatranscriptomeActivity A metatranscriptome activity that e MetatranscriptomeAnnotationActivity MetatranscriptomeAssembly NomAnalysisActivity ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... AttributeValue The value for any value of a attribute for a sample BooleanValue A value that is a boolean ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image InstrumentValue IntegerValue A value that is an integer PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp UrlValue A value that is a string that conforms to URL syntax CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data DissolvingActivity FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome LabDevice MagBin MaterialContainer MaterialSamplingActivity MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... NamedThing a databased entity or concept/class DataObject An object that primarily consists of symbols that represent information GeneProduct A molecule encoded by a gene that has an evolved function Instrument A material entity that is designed to perform a function in a scientific inve... MaterialEntity AnalyticalSample Biosample Biological source material which can be characterized by an experiment ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected MaterialSample OntologyClass ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... Reaction An individual biochemical transformation carried out by a functional unit of ... PlannedProcess BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... Extraction A material separation in which a desired component of an input material is se... LibraryPreparation Pooling physical combination of several instances of like material CollectingBiosamplesFromSite OmicsProcessing The methods and processes used to generate omics data from a biosample or org... Study A study summarizes the overall goal of a research initiative and outlines the... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol QualityControlReport ReactionActivity ReactionParticipant Instances of this link a reaction to a chemical entity participant"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture activity_set This property links a database object to the set of workflow activities activity_speed activity_temperature activity_time add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternate_emails One or more other email addresses for an entity alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_collected amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_role applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers atmospheric_data Measurement of atmospheric data; can include multiple data attribute A attribute of a biosample avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... award_dois One or more DOIs that links a study, or similar entiry, to information about ... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name bin_quality binned_contig_num biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... calcium Concentration of calcium in the sample canary a slot that can be added and removed as evidence that schema changes have pro... carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical from reaction participant class chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collected_into collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness completion_date compression_type If provided, specifies the compression type conduc Electrical conductivity of water container_size container_type contamination contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object dataset_dois One or more DOIs that links a study, or similar entity, to the generated data date_created from database class date_last_rain The date of the last time it rained density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing device_type dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids direction One of l->r, r->l, bidirectional, neutral display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dissolution_aided_by dissolution_reagent dissolution_volume dissolved_in dissolving_activity_set dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna dois A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_dois One or more DOIs that links to an EMSL Research Campaign page emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ess_dive_datasets List of ESS-DIVE dataset DOIs ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class execution_resource exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_method extraction_set This property links a database object to the set of extractions within it extraction_target extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_method Type of filter used or how the sample was filtered filter_type A device which removes solid particulates or airborne molecular contaminants fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count gene_function_id genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis project in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class gtdbtk_domain gtdbtk_family gtdbtk_genus gtdbtk_order gtdbtk_phylum gtdbtk_species habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_numeric_value has_raw_value has_unit Example \"m\" has_boolean_value Links a quantity value to a boolean has_calibration A reference to a file that holds calibration information has_credit_associations This slot links a study to a credit association has_function has_input An input to a process has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_quantifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output biosample to a processing step has_part A pathway can be broken down to a series of reaction step has_participants has_peptide_quantifications has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_name The name of the instrument that was used for processing the sample int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... investigation_field field describing aspect of the investigation/study to which the sample belong... is_balanced is_diastereoselective is_fully_characterized False if includes R-groups is_stereo is_transport isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... keywords A list of keywords that used to associate the entity language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation left_participants library_preparation_kit library_preparation_set This property links a database object to the set of DNA extractions within it library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num magnesium Concentration of magnesium in the sample mags_activity_set This property links a database object to the set of MAGs analysis activities mags_list manganese Concentration of manganese in the sample massive_identifiers identifiers for entities according to MASSIVE massive_study_identifiers identifiers for corresponding study in MASSIVE material_input material_output material_sample_set material_sampling_activity_set max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id metabolite_quantified the specific metabolite identifier metabolomics_analysis_activity_set This property links a database object to the set of metabolomics analysis act... metagenome_annotation_activity_set This property links a database object to the set of metagenome annotation act... metagenome_annotation_id metagenome_assembly_parameter metagenome_assembly_set This property links a database object to the set of metagenome assembly activ... metagenome_sequencing_activity_set This property links a database object to the set of metagenome sequencing act... metaproteomics_analysis_activity_set This property links a database object to the set of metaproteomics analysis a... metatranscriptome_activity_set This property links a database object to the set of metatranscriptome analysi... methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_deims_sdr_link neon_eco_type neon_identifiers identifiers for entities according to NEON neon_soil_type neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) nom_analysis_activity_set This property links a database object to the set of natural organic matter (N... non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes from study class nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field nucleic_acid_concentration num_16s num_23s num_5s num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna number_of_contig number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_processing_set This property links a database object to the set of omics processings within ... omics_type The type of omics data orcid The ORCID of a person org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed pooling_set porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_link publication_dois One or more DOIs that links a study, or similar entity, to a publication publications A list of publications that are associated with the entity quad_pos The quadrant position of the sampling room within the building quality_control_report radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reaction_activity_set reaction_aided_by reaction_temperature reaction_time reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_based_taxonomy_analysis_activity_set This property links a database object to the set of read based analysis activ... read_qc_analysis_activity_set This property links a database object to the set of read QC analysis activiti... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... relevant_protocols replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... right_participants rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_type Type of sample being submitted sampling_method saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smarts_string smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time status stoichiometry from reaction participant class store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type An optional string that specifies the type object unbinned_contig_num url used ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum ArchStrucEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ContainerTypeEnum CreditEnum CurLandUseEnum DeposEnvEnum DeviceTypeEnum DnaSampleFormatEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum IntWallCondEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum MechStrucEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum ProcessingInstitutionEnum ProfilePositionEnum QuadPosEnum RelSampLocEnum RnaSampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SampleTypeEnum SamplingMethodEnum SeasonUseEnum SedimentTypeEnum ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SolventEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StatusEnum StudyCategoryEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description Checklist A MIxS checklist ChecklistPackageCombination A combination of a checklist and a package DataObjectSubset Subset consisting of the data objects that either inputs or outputs of proces... Environment Investigation MixsExtension MixsEnvironmentalTriad NucleicAcidSequenceSource Package A MIxS package SampleSubset Subset consisting of entities linked to the processing of samples Sequencing WorkflowSubset Subset consisting of just the workflow execution activities"},{"location":"Activity/","title":"Class: Activity","text":"a provence-generating activity
URI: nmdc:Activity
classDiagram\n class Activity\n Activity <|-- WorkflowExecutionActivity\n\n Activity : ended_at_time\n\n Activity : id\n\n Activity : name\n\n Activity : started_at_time\n\n Activity : used\n\n Activity : was_informed_by\n\n Activity --|> Activity : was_informed_by\n\n\nname: Activity\ndescription: a provence-generating activity\nnotes:\n- removed was_associated_with because we are trying to avoid instantiating id-less\n Agents\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:Activity\nslots:\n- id\n- name\n- started_at_time\n- ended_at_time\n- was_informed_by\n- used\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Activity\ndescription: a provence-generating activity\nnotes:\n- removed was_associated_with because we are trying to avoid instantiating id-less\n Agents\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:Activity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Activity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Activity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: Activity\n domain_of:\n - Activity\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: Activity\n domain_of:\n - Activity\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: Activity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: Activity\n domain_of:\n - Activity\n range: string\n\nURI: AnalysisTypeEnum
"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None metaproteomics None metatranscriptomics None natural organic matter None"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":"name: analysis_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metabolomics:\n text: metabolomics\n metagenomics:\n text: metagenomics\n metaproteomics:\n text: metaproteomics\n metatranscriptomics:\n text: metatranscriptomics\n natural organic matter:\n text: natural organic matter\n\nURI: nmdc:AnalyticalSample
classDiagram\n class AnalyticalSample\n MaterialEntity <|-- AnalyticalSample\n\n AnalyticalSample : alternative_identifiers\n\n AnalyticalSample : description\n\n AnalyticalSample : id\n\n AnalyticalSample : name\n\n\nname: AnalyticalSample\ntitle: Analytical Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: AnalyticalSample\ntitle: Analytical Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: AnalyticalSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: AnalyticalSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: AnalyticalSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: AnalyticalSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ArchStrucEnum
"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":"name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building:\n text: building\n shed:\n text: shed\n home:\n text: home\n\nThe value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value
URI: nmdc:AttributeValue
classDiagram\n class AttributeValue\n AttributeValue <|-- InstrumentValue\n AttributeValue <|-- QuantityValue\n AttributeValue <|-- ImageValue\n AttributeValue <|-- PersonValue\n AttributeValue <|-- TextValue\n AttributeValue <|-- UrlValue\n AttributeValue <|-- TimestampValue\n AttributeValue <|-- IntegerValue\n AttributeValue <|-- BooleanValue\n AttributeValue <|-- ControlledTermValue\n AttributeValue <|-- GeolocationValue\n\n AttributeValue : has_raw_value\n\n AttributeValue : was_generated_by\n\n AttributeValue --|> Activity : was_generated_by\n\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- has_raw_value\n- was_generated_by\nslot_usage:\n type:\n name: type\n description: An optional string that specified the type of object.\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n type:\n name: type\n description: An optional string that specified the type of object.\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: AttributeValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: AttributeValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: BiolStatEnum
"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":"name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n wild:\n text: wild\n natural:\n text: natural\n semi-natural:\n text: semi-natural\n inbred line:\n text: inbred line\n breeder's line:\n text: breeder's line\n hybrid:\n text: hybrid\n clonal selection:\n text: clonal selection\n mutant:\n text: mutant\n\nBiological source material which can be characterized by an experiment.
URI: nmdc:Biosample
classDiagram\n class Biosample\n MaterialEntity <|-- Biosample\n\n Biosample : abs_air_humidity\n\n Biosample --|> QuantityValue : abs_air_humidity\n\n Biosample : add_date\n\n Biosample : add_recov_method\n\n Biosample --|> TextValue : add_recov_method\n\n Biosample : additional_info\n\n Biosample --|> TextValue : additional_info\n\n Biosample : address\n\n Biosample --|> TextValue : address\n\n Biosample : adj_room\n\n Biosample --|> TextValue : adj_room\n\n Biosample : aero_struc\n\n Biosample --|> TextValue : aero_struc\n\n Biosample : agrochem_addition\n\n Biosample --|> TextValue : agrochem_addition\n\n Biosample : air_PM_concen\n\n Biosample --|> TextValue : air_PM_concen\n\n Biosample : air_temp\n\n Biosample --|> QuantityValue : air_temp\n\n Biosample : air_temp_regm\n\n Biosample --|> TextValue : air_temp_regm\n\n Biosample : al_sat\n\n Biosample --|> QuantityValue : al_sat\n\n Biosample : al_sat_meth\n\n Biosample --|> TextValue : al_sat_meth\n\n Biosample : alkalinity\n\n Biosample --|> QuantityValue : alkalinity\n\n Biosample : alkalinity_method\n\n Biosample --|> TextValue : alkalinity_method\n\n Biosample : alkyl_diethers\n\n Biosample --|> QuantityValue : alkyl_diethers\n\n Biosample : alt\n\n Biosample --|> QuantityValue : alt\n\n Biosample : alternative_identifiers\n\n Biosample : aminopept_act\n\n Biosample --|> QuantityValue : aminopept_act\n\n Biosample : ammonium\n\n Biosample --|> QuantityValue : ammonium\n\n Biosample : ammonium_nitrogen\n\n Biosample --|> QuantityValue : ammonium_nitrogen\n\n Biosample : amount_light\n\n Biosample --|> QuantityValue : amount_light\n\n Biosample : analysis_type\n\n Biosample --|> analysis_type_enum : analysis_type\n\n Biosample : ances_data\n\n Biosample --|> TextValue : ances_data\n\n Biosample : annual_precpt\n\n Biosample --|> QuantityValue : annual_precpt\n\n Biosample : annual_temp\n\n Biosample --|> QuantityValue : annual_temp\n\n Biosample : antibiotic_regm\n\n Biosample --|> TextValue : antibiotic_regm\n\n Biosample : api\n\n Biosample --|> QuantityValue : api\n\n Biosample : arch_struc\n\n Biosample --|> arch_struc_enum : arch_struc\n\n Biosample : aromatics_pc\n\n Biosample --|> TextValue : aromatics_pc\n\n Biosample : asphaltenes_pc\n\n Biosample --|> TextValue : asphaltenes_pc\n\n Biosample : atmospheric_data\n\n Biosample --|> TextValue : atmospheric_data\n\n Biosample : avg_dew_point\n\n Biosample --|> QuantityValue : avg_dew_point\n\n Biosample : avg_occup\n\n Biosample --|> TextValue : avg_occup\n\n Biosample : avg_temp\n\n Biosample --|> QuantityValue : avg_temp\n\n Biosample : bac_prod\n\n Biosample --|> QuantityValue : bac_prod\n\n Biosample : bac_resp\n\n Biosample --|> QuantityValue : bac_resp\n\n Biosample : bacteria_carb_prod\n\n Biosample --|> QuantityValue : bacteria_carb_prod\n\n Biosample : barometric_press\n\n Biosample --|> QuantityValue : barometric_press\n\n Biosample : basin\n\n Biosample --|> TextValue : basin\n\n Biosample : bathroom_count\n\n Biosample --|> TextValue : bathroom_count\n\n Biosample : bedroom_count\n\n Biosample --|> TextValue : bedroom_count\n\n Biosample : benzene\n\n Biosample --|> QuantityValue : benzene\n\n Biosample : biochem_oxygen_dem\n\n Biosample --|> QuantityValue : biochem_oxygen_dem\n\n Biosample : biocide\n\n Biosample --|> TextValue : biocide\n\n Biosample : biocide_admin_method\n\n Biosample --|> TextValue : biocide_admin_method\n\n Biosample : biol_stat\n\n Biosample --|> biol_stat_enum : biol_stat\n\n Biosample : biomass\n\n Biosample --|> TextValue : biomass\n\n Biosample : biosample_categories\n\n Biosample --|> BiosampleCategoryEnum : biosample_categories\n\n Biosample : biotic_regm\n\n Biosample --|> TextValue : biotic_regm\n\n Biosample : biotic_relationship\n\n Biosample --|> biotic_relationship_enum : biotic_relationship\n\n Biosample : bishomohopanol\n\n Biosample --|> QuantityValue : bishomohopanol\n\n Biosample : blood_press_diast\n\n Biosample --|> QuantityValue : blood_press_diast\n\n Biosample : blood_press_syst\n\n Biosample --|> QuantityValue : blood_press_syst\n\n Biosample : bromide\n\n Biosample --|> QuantityValue : bromide\n\n Biosample : build_docs\n\n Biosample --|> build_docs_enum : build_docs\n\n Biosample : build_occup_type\n\n Biosample --|> build_occup_type_enum : build_occup_type\n\n Biosample : building_setting\n\n Biosample --|> building_setting_enum : building_setting\n\n Biosample : built_struc_age\n\n Biosample --|> QuantityValue : built_struc_age\n\n Biosample : built_struc_set\n\n Biosample --|> TextValue : built_struc_set\n\n Biosample : built_struc_type\n\n Biosample --|> TextValue : built_struc_type\n\n Biosample : calcium\n\n Biosample --|> QuantityValue : calcium\n\n Biosample : carb_dioxide\n\n Biosample --|> QuantityValue : carb_dioxide\n\n Biosample : carb_monoxide\n\n Biosample --|> QuantityValue : carb_monoxide\n\n Biosample : carb_nitro_ratio\n\n Biosample --|> QuantityValue : carb_nitro_ratio\n\n Biosample : ceil_area\n\n Biosample --|> QuantityValue : ceil_area\n\n Biosample : ceil_cond\n\n Biosample --|> ceil_cond_enum : ceil_cond\n\n Biosample : ceil_finish_mat\n\n Biosample --|> ceil_finish_mat_enum : ceil_finish_mat\n\n Biosample : ceil_struc\n\n Biosample --|> TextValue : ceil_struc\n\n Biosample : ceil_texture\n\n Biosample --|> ceil_texture_enum : ceil_texture\n\n Biosample : ceil_thermal_mass\n\n Biosample --|> QuantityValue : ceil_thermal_mass\n\n Biosample : ceil_type\n\n Biosample --|> ceil_type_enum : ceil_type\n\n Biosample : ceil_water_mold\n\n Biosample --|> TextValue : ceil_water_mold\n\n Biosample : chem_administration\n\n Biosample --|> ControlledTermValue : chem_administration\n\n Biosample : chem_mutagen\n\n Biosample --|> TextValue : chem_mutagen\n\n Biosample : chem_oxygen_dem\n\n Biosample --|> QuantityValue : chem_oxygen_dem\n\n Biosample : chem_treat_method\n\n Biosample : chem_treatment\n\n Biosample --|> TextValue : chem_treatment\n\n Biosample : chimera_check\n\n Biosample --|> TextValue : chimera_check\n\n Biosample : chloride\n\n Biosample --|> QuantityValue : chloride\n\n Biosample : chlorophyll\n\n Biosample --|> QuantityValue : chlorophyll\n\n Biosample : climate_environment\n\n Biosample --|> TextValue : climate_environment\n\n Biosample : collected_from\n\n Biosample --|> FieldResearchSite : collected_from\n\n Biosample : collection_date\n\n Biosample --|> TimestampValue : collection_date\n\n Biosample : collection_date_inc\n\n Biosample : collection_time\n\n Biosample : collection_time_inc\n\n Biosample : community\n\n Biosample : conduc\n\n Biosample --|> QuantityValue : conduc\n\n Biosample : cool_syst_id\n\n Biosample --|> TextValue : cool_syst_id\n\n Biosample : core_field\n\n Biosample : crop_rotation\n\n Biosample --|> TextValue : crop_rotation\n\n Biosample : cult_root_med\n\n Biosample --|> TextValue : cult_root_med\n\n Biosample : cur_land_use\n\n Biosample --|> cur_land_use_enum : cur_land_use\n\n Biosample : cur_vegetation\n\n Biosample --|> TextValue : cur_vegetation\n\n Biosample : cur_vegetation_meth\n\n Biosample --|> TextValue : cur_vegetation_meth\n\n Biosample : date_last_rain\n\n Biosample --|> TimestampValue : date_last_rain\n\n Biosample : density\n\n Biosample --|> QuantityValue : density\n\n Biosample : depos_env\n\n Biosample --|> depos_env_enum : depos_env\n\n Biosample : depth\n\n Biosample --|> QuantityValue : depth\n\n Biosample : description\n\n Biosample : dew_point\n\n Biosample --|> QuantityValue : dew_point\n\n Biosample : diether_lipids\n\n Biosample --|> TextValue : diether_lipids\n\n Biosample : diss_carb_dioxide\n\n Biosample --|> QuantityValue : diss_carb_dioxide\n\n Biosample : diss_hydrogen\n\n Biosample --|> QuantityValue : diss_hydrogen\n\n Biosample : diss_inorg_carb\n\n Biosample --|> QuantityValue : diss_inorg_carb\n\n Biosample : diss_inorg_nitro\n\n Biosample --|> QuantityValue : diss_inorg_nitro\n\n Biosample : diss_inorg_phosp\n\n Biosample --|> QuantityValue : diss_inorg_phosp\n\n Biosample : diss_iron\n\n Biosample --|> QuantityValue : diss_iron\n\n Biosample : diss_org_carb\n\n Biosample --|> QuantityValue : diss_org_carb\n\n Biosample : diss_org_nitro\n\n Biosample --|> QuantityValue : diss_org_nitro\n\n Biosample : diss_oxygen\n\n Biosample --|> QuantityValue : diss_oxygen\n\n Biosample : diss_oxygen_fluid\n\n Biosample --|> QuantityValue : diss_oxygen_fluid\n\n Biosample : dna_absorb1\n\n Biosample : dna_absorb2\n\n Biosample : dna_collect_site\n\n Biosample : dna_concentration\n\n Biosample : dna_cont_type\n\n Biosample --|> JgiContTypeEnum : dna_cont_type\n\n Biosample : dna_cont_well\n\n Biosample : dna_container_id\n\n Biosample : dna_dnase\n\n Biosample --|> YesNoEnum : dna_dnase\n\n Biosample : dna_isolate_meth\n\n Biosample : dna_organisms\n\n Biosample : dna_project_contact\n\n Biosample : dna_samp_id\n\n Biosample : dna_sample_format\n\n Biosample --|> dna_sample_format_enum : dna_sample_format\n\n Biosample : dna_sample_name\n\n Biosample : dna_seq_project\n\n Biosample : dna_seq_project_name\n\n Biosample : dna_seq_project_pi\n\n Biosample : dna_volume\n\n Biosample : dnase_rna\n\n Biosample --|> YesNoEnum : dnase_rna\n\n Biosample : door_comp_type\n\n Biosample --|> door_comp_type_enum : door_comp_type\n\n Biosample : door_cond\n\n Biosample --|> door_cond_enum : door_cond\n\n Biosample : door_direct\n\n Biosample --|> door_direct_enum : door_direct\n\n Biosample : door_loc\n\n Biosample --|> door_loc_enum : door_loc\n\n Biosample : door_mat\n\n Biosample --|> door_mat_enum : door_mat\n\n Biosample : door_move\n\n Biosample --|> door_move_enum : door_move\n\n Biosample : door_size\n\n Biosample --|> QuantityValue : door_size\n\n Biosample : door_type\n\n Biosample --|> door_type_enum : door_type\n\n Biosample : door_type_metal\n\n Biosample --|> door_type_metal_enum : door_type_metal\n\n Biosample : door_type_wood\n\n Biosample --|> door_type_wood_enum : door_type_wood\n\n Biosample : door_water_mold\n\n Biosample --|> TextValue : door_water_mold\n\n Biosample : down_par\n\n Biosample --|> QuantityValue : down_par\n\n Biosample : drainage_class\n\n Biosample --|> drainage_class_enum : drainage_class\n\n Biosample : drawings\n\n Biosample --|> drawings_enum : drawings\n\n Biosample : ecosystem\n\n Biosample : ecosystem_category\n\n Biosample : ecosystem_subtype\n\n Biosample : ecosystem_type\n\n Biosample : efficiency_percent\n\n Biosample --|> QuantityValue : efficiency_percent\n\n Biosample : elev\n\n Biosample : elevator\n\n Biosample --|> TextValue : elevator\n\n Biosample : embargoed\n\n Biosample : emsl_biosample_identifiers\n\n Biosample : emulsions\n\n Biosample --|> TextValue : emulsions\n\n Biosample : env_broad_scale\n\n Biosample --|> ControlledIdentifiedTermValue : env_broad_scale\n\n Biosample : env_local_scale\n\n Biosample --|> ControlledIdentifiedTermValue : env_local_scale\n\n Biosample : env_medium\n\n Biosample --|> ControlledIdentifiedTermValue : env_medium\n\n Biosample : env_package\n\n Biosample --|> TextValue : env_package\n\n Biosample : environment_field\n\n Biosample : escalator\n\n Biosample --|> TextValue : escalator\n\n Biosample : ethylbenzene\n\n Biosample --|> QuantityValue : ethylbenzene\n\n Biosample : exp_duct\n\n Biosample --|> QuantityValue : exp_duct\n\n Biosample : exp_pipe\n\n Biosample --|> QuantityValue : exp_pipe\n\n Biosample : experimental_factor\n\n Biosample --|> ControlledTermValue : experimental_factor\n\n Biosample : experimental_factor_other\n\n Biosample : ext_door\n\n Biosample --|> TextValue : ext_door\n\n Biosample : ext_wall_orient\n\n Biosample --|> ext_wall_orient_enum : ext_wall_orient\n\n Biosample : ext_window_orient\n\n Biosample --|> ext_window_orient_enum : ext_window_orient\n\n Biosample : extreme_event\n\n Biosample : fao_class\n\n Biosample --|> fao_class_enum : fao_class\n\n Biosample : fertilizer_regm\n\n Biosample --|> TextValue : fertilizer_regm\n\n Biosample : field\n\n Biosample --|> TextValue : field\n\n Biosample : filter_method\n\n Biosample : filter_type\n\n Biosample --|> filter_type_enum : filter_type\n\n Biosample : fire\n\n Biosample : fireplace_type\n\n Biosample --|> TextValue : fireplace_type\n\n Biosample : flooding\n\n Biosample : floor_age\n\n Biosample --|> QuantityValue : floor_age\n\n Biosample : floor_area\n\n Biosample --|> QuantityValue : floor_area\n\n Biosample : floor_cond\n\n Biosample --|> floor_cond_enum : floor_cond\n\n Biosample : floor_count\n\n Biosample --|> TextValue : floor_count\n\n Biosample : floor_finish_mat\n\n Biosample --|> floor_finish_mat_enum : floor_finish_mat\n\n Biosample : floor_struc\n\n Biosample --|> floor_struc_enum : floor_struc\n\n Biosample : floor_thermal_mass\n\n Biosample --|> QuantityValue : floor_thermal_mass\n\n Biosample : floor_water_mold\n\n Biosample --|> floor_water_mold_enum : floor_water_mold\n\n Biosample : fluor\n\n Biosample --|> QuantityValue : fluor\n\n Biosample : freq_clean\n\n Biosample --|> QuantityValue : freq_clean\n\n Biosample : freq_cook\n\n Biosample --|> QuantityValue : freq_cook\n\n Biosample : fungicide_regm\n\n Biosample --|> TextValue : fungicide_regm\n\n Biosample : furniture\n\n Biosample --|> furniture_enum : furniture\n\n Biosample : gaseous_environment\n\n Biosample --|> TextValue : gaseous_environment\n\n Biosample : gaseous_substances\n\n Biosample --|> TextValue : gaseous_substances\n\n Biosample : gender_restroom\n\n Biosample --|> gender_restroom_enum : gender_restroom\n\n Biosample : genetic_mod\n\n Biosample --|> TextValue : genetic_mod\n\n Biosample : geo_loc_name\n\n Biosample --|> TextValue : geo_loc_name\n\n Biosample : glucosidase_act\n\n Biosample --|> QuantityValue : glucosidase_act\n\n Biosample : gold_biosample_identifiers\n\n Biosample : gravidity\n\n Biosample --|> TextValue : gravidity\n\n Biosample : gravity\n\n Biosample --|> TextValue : gravity\n\n Biosample : growth_facil\n\n Biosample --|> ControlledTermValue : growth_facil\n\n Biosample : growth_habit\n\n Biosample --|> growth_habit_enum : growth_habit\n\n Biosample : growth_hormone_regm\n\n Biosample --|> TextValue : growth_hormone_regm\n\n Biosample : habitat\n\n Biosample : hall_count\n\n Biosample --|> TextValue : hall_count\n\n Biosample : handidness\n\n Biosample --|> handidness_enum : handidness\n\n Biosample : has_numeric_value\n\n Biosample : has_raw_value\n\n Biosample : has_unit\n\n Biosample : hc_produced\n\n Biosample --|> hc_produced_enum : hc_produced\n\n Biosample : hcr\n\n Biosample --|> hcr_enum : hcr\n\n Biosample : hcr_fw_salinity\n\n Biosample --|> QuantityValue : hcr_fw_salinity\n\n Biosample : hcr_geol_age\n\n Biosample --|> hcr_geol_age_enum : hcr_geol_age\n\n Biosample : hcr_pressure\n\n Biosample --|> TextValue : hcr_pressure\n\n Biosample : hcr_temp\n\n Biosample --|> TextValue : hcr_temp\n\n Biosample : heat_cool_type\n\n Biosample --|> heat_cool_type_enum : heat_cool_type\n\n Biosample : heat_deliv_loc\n\n Biosample --|> heat_deliv_loc_enum : heat_deliv_loc\n\n Biosample : heat_sys_deliv_meth\n\n Biosample : heat_system_id\n\n Biosample --|> TextValue : heat_system_id\n\n Biosample : heavy_metals\n\n Biosample --|> TextValue : heavy_metals\n\n Biosample : heavy_metals_meth\n\n Biosample --|> TextValue : heavy_metals_meth\n\n Biosample : height_carper_fiber\n\n Biosample --|> QuantityValue : height_carper_fiber\n\n Biosample : herbicide_regm\n\n Biosample --|> TextValue : herbicide_regm\n\n Biosample : horizon_meth\n\n Biosample --|> TextValue : horizon_meth\n\n Biosample : host_age\n\n Biosample --|> QuantityValue : host_age\n\n Biosample : host_body_habitat\n\n Biosample --|> TextValue : host_body_habitat\n\n Biosample : host_body_product\n\n Biosample --|> ControlledTermValue : host_body_product\n\n Biosample : host_body_site\n\n Biosample --|> ControlledTermValue : host_body_site\n\n Biosample : host_body_temp\n\n Biosample --|> QuantityValue : host_body_temp\n\n Biosample : host_color\n\n Biosample --|> TextValue : host_color\n\n Biosample : host_common_name\n\n Biosample --|> TextValue : host_common_name\n\n Biosample : host_diet\n\n Biosample --|> TextValue : host_diet\n\n Biosample : host_dry_mass\n\n Biosample --|> QuantityValue : host_dry_mass\n\n Biosample : host_family_relation\n\n Biosample : host_genotype\n\n Biosample --|> TextValue : host_genotype\n\n Biosample : host_growth_cond\n\n Biosample --|> TextValue : host_growth_cond\n\n Biosample : host_height\n\n Biosample --|> QuantityValue : host_height\n\n Biosample : host_last_meal\n\n Biosample --|> TextValue : host_last_meal\n\n Biosample : host_length\n\n Biosample --|> QuantityValue : host_length\n\n Biosample : host_life_stage\n\n Biosample --|> TextValue : host_life_stage\n\n Biosample : host_name\n\n Biosample : host_phenotype\n\n Biosample --|> ControlledTermValue : host_phenotype\n\n Biosample : host_sex\n\n Biosample --|> host_sex_enum : host_sex\n\n Biosample : host_shape\n\n Biosample --|> TextValue : host_shape\n\n Biosample : host_subject_id\n\n Biosample --|> TextValue : host_subject_id\n\n Biosample : host_subspecf_genlin\n\n Biosample : host_substrate\n\n Biosample --|> TextValue : host_substrate\n\n Biosample : host_symbiont\n\n Biosample : host_taxid\n\n Biosample --|> ControlledIdentifiedTermValue : host_taxid\n\n Biosample : host_tot_mass\n\n Biosample --|> QuantityValue : host_tot_mass\n\n Biosample : host_wet_mass\n\n Biosample --|> QuantityValue : host_wet_mass\n\n Biosample : humidity\n\n Biosample --|> QuantityValue : humidity\n\n Biosample : humidity_regm\n\n Biosample --|> TextValue : humidity_regm\n\n Biosample : id\n\n Biosample : igsn_biosample_identifiers\n\n Biosample : img_identifiers\n\n Biosample : indoor_space\n\n Biosample --|> indoor_space_enum : indoor_space\n\n Biosample : indoor_surf\n\n Biosample --|> indoor_surf_enum : indoor_surf\n\n Biosample : indust_eff_percent\n\n Biosample --|> QuantityValue : indust_eff_percent\n\n Biosample : inorg_particles\n\n Biosample --|> TextValue : inorg_particles\n\n Biosample : insdc_biosample_identifiers\n\n Biosample : inside_lux\n\n Biosample --|> QuantityValue : inside_lux\n\n Biosample : int_wall_cond\n\n Biosample --|> int_wall_cond_enum : int_wall_cond\n\n Biosample : investigation_field\n\n Biosample : isotope_exposure\n\n Biosample : iw_bt_date_well\n\n Biosample --|> TimestampValue : iw_bt_date_well\n\n Biosample : iwf\n\n Biosample --|> QuantityValue : iwf\n\n Biosample : last_clean\n\n Biosample --|> TimestampValue : last_clean\n\n Biosample : lat_lon\n\n Biosample --|> GeolocationValue : lat_lon\n\n Biosample : lbc_thirty\n\n Biosample --|> QuantityValue : lbc_thirty\n\n Biosample : lbceq\n\n Biosample --|> QuantityValue : lbceq\n\n Biosample : light_intensity\n\n Biosample --|> QuantityValue : light_intensity\n\n Biosample : light_regm\n\n Biosample --|> TextValue : light_regm\n\n Biosample : light_type\n\n Biosample --|> light_type_enum : light_type\n\n Biosample : link_addit_analys\n\n Biosample --|> TextValue : link_addit_analys\n\n Biosample : link_class_info\n\n Biosample --|> TextValue : link_class_info\n\n Biosample : link_climate_info\n\n Biosample --|> TextValue : link_climate_info\n\n Biosample : lithology\n\n Biosample --|> lithology_enum : lithology\n\n Biosample : local_class\n\n Biosample --|> TextValue : local_class\n\n Biosample : local_class_meth\n\n Biosample --|> TextValue : local_class_meth\n\n Biosample : location\n\n Biosample : magnesium\n\n Biosample --|> QuantityValue : magnesium\n\n Biosample : manganese\n\n Biosample --|> QuantityValue : manganese\n\n Biosample : max_occup\n\n Biosample --|> QuantityValue : max_occup\n\n Biosample : mean_frict_vel\n\n Biosample --|> QuantityValue : mean_frict_vel\n\n Biosample : mean_peak_frict_vel\n\n Biosample --|> QuantityValue : mean_peak_frict_vel\n\n Biosample : mech_struc\n\n Biosample --|> mech_struc_enum : mech_struc\n\n Biosample : mechanical_damage\n\n Biosample --|> TextValue : mechanical_damage\n\n Biosample : methane\n\n Biosample --|> QuantityValue : methane\n\n Biosample : micro_biomass_c_meth\n\n Biosample : micro_biomass_meth\n\n Biosample : micro_biomass_n_meth\n\n Biosample : microbial_biomass\n\n Biosample --|> QuantityValue : microbial_biomass\n\n Biosample : microbial_biomass_c\n\n Biosample : microbial_biomass_n\n\n Biosample : mineral_nutr_regm\n\n Biosample --|> TextValue : mineral_nutr_regm\n\n Biosample : misc_param\n\n Biosample --|> TextValue : misc_param\n\n Biosample : mod_date\n\n Biosample : n_alkanes\n\n Biosample --|> TextValue : n_alkanes\n\n Biosample : name\n\n Biosample : ncbi_taxonomy_name\n\n Biosample : neon_biosample_identifiers\n\n Biosample : nitrate\n\n Biosample --|> QuantityValue : nitrate\n\n Biosample : nitrate_nitrogen\n\n Biosample --|> QuantityValue : nitrate_nitrogen\n\n Biosample : nitrite\n\n Biosample --|> QuantityValue : nitrite\n\n Biosample : nitrite_nitrogen\n\n Biosample --|> QuantityValue : nitrite_nitrogen\n\n Biosample : nitro\n\n Biosample --|> QuantityValue : nitro\n\n Biosample : non_microb_biomass\n\n Biosample : non_microb_biomass_method\n\n Biosample : non_min_nutr_regm\n\n Biosample : nucl_acid_amp\n\n Biosample --|> TextValue : nucl_acid_amp\n\n Biosample : nucl_acid_ext\n\n Biosample --|> TextValue : nucl_acid_ext\n\n Biosample : nucleic_acid_sequence_source_field\n\n Biosample : number_pets\n\n Biosample --|> QuantityValue : number_pets\n\n Biosample : number_plants\n\n Biosample --|> QuantityValue : number_plants\n\n Biosample : number_resident\n\n Biosample --|> QuantityValue : number_resident\n\n Biosample : occup_density_samp\n\n Biosample --|> QuantityValue : occup_density_samp\n\n Biosample : occup_document\n\n Biosample --|> occup_document_enum : occup_document\n\n Biosample : occup_samp\n\n Biosample --|> QuantityValue : occup_samp\n\n Biosample : org_carb\n\n Biosample --|> QuantityValue : org_carb\n\n Biosample : org_count_qpcr_info\n\n Biosample : org_matter\n\n Biosample --|> QuantityValue : org_matter\n\n Biosample : org_nitro\n\n Biosample --|> QuantityValue : org_nitro\n\n Biosample : org_nitro_method\n\n Biosample : org_particles\n\n Biosample --|> TextValue : org_particles\n\n Biosample : organism_count\n\n Biosample --|> QuantityValue : organism_count\n\n Biosample : other_treatment\n\n Biosample : owc_tvdss\n\n Biosample --|> QuantityValue : owc_tvdss\n\n Biosample : oxy_stat_samp\n\n Biosample --|> oxy_stat_samp_enum : oxy_stat_samp\n\n Biosample : oxygen\n\n Biosample --|> QuantityValue : oxygen\n\n Biosample : part_of\n\n Biosample --|> Study : part_of\n\n Biosample : part_org_carb\n\n Biosample --|> QuantityValue : part_org_carb\n\n Biosample : part_org_nitro\n\n Biosample --|> QuantityValue : part_org_nitro\n\n Biosample : particle_class\n\n Biosample --|> TextValue : particle_class\n\n Biosample : pcr_cond\n\n Biosample --|> TextValue : pcr_cond\n\n Biosample : pcr_primers\n\n Biosample --|> TextValue : pcr_primers\n\n Biosample : permeability\n\n Biosample --|> TextValue : permeability\n\n Biosample : perturbation\n\n Biosample --|> TextValue : perturbation\n\n Biosample : pesticide_regm\n\n Biosample --|> TextValue : pesticide_regm\n\n Biosample : petroleum_hydrocarb\n\n Biosample --|> QuantityValue : petroleum_hydrocarb\n\n Biosample : ph\n\n Biosample : ph_meth\n\n Biosample --|> TextValue : ph_meth\n\n Biosample : ph_regm\n\n Biosample --|> TextValue : ph_regm\n\n Biosample : phaeopigments\n\n Biosample --|> TextValue : phaeopigments\n\n Biosample : phosphate\n\n Biosample --|> QuantityValue : phosphate\n\n Biosample : phosplipid_fatt_acid\n\n Biosample --|> TextValue : phosplipid_fatt_acid\n\n Biosample : photon_flux\n\n Biosample --|> QuantityValue : photon_flux\n\n Biosample : plant_growth_med\n\n Biosample --|> ControlledTermValue : plant_growth_med\n\n Biosample : plant_product\n\n Biosample --|> TextValue : plant_product\n\n Biosample : plant_sex\n\n Biosample --|> plant_sex_enum : plant_sex\n\n Biosample : plant_struc\n\n Biosample --|> ControlledTermValue : plant_struc\n\n Biosample : pollutants\n\n Biosample --|> TextValue : pollutants\n\n Biosample : pool_dna_extracts\n\n Biosample --|> TextValue : pool_dna_extracts\n\n Biosample : porosity\n\n Biosample --|> TextValue : porosity\n\n Biosample : potassium\n\n Biosample --|> QuantityValue : potassium\n\n Biosample : pour_point\n\n Biosample --|> QuantityValue : pour_point\n\n Biosample : pre_treatment\n\n Biosample --|> TextValue : pre_treatment\n\n Biosample : pres_animal_insect\n\n Biosample : pressure\n\n Biosample --|> QuantityValue : pressure\n\n Biosample : prev_land_use_meth\n\n Biosample : previous_land_use\n\n Biosample --|> TextValue : previous_land_use\n\n Biosample : primary_prod\n\n Biosample --|> QuantityValue : primary_prod\n\n Biosample : primary_treatment\n\n Biosample --|> TextValue : primary_treatment\n\n Biosample : prod_rate\n\n Biosample --|> QuantityValue : prod_rate\n\n Biosample : prod_start_date\n\n Biosample --|> TimestampValue : prod_start_date\n\n Biosample : profile_position\n\n Biosample --|> profile_position_enum : profile_position\n\n Biosample : project_id\n\n Biosample : proport_woa_temperature\n\n Biosample : proposal_dna\n\n Biosample : proposal_rna\n\n Biosample : quad_pos\n\n Biosample --|> quad_pos_enum : quad_pos\n\n Biosample : radiation_regm\n\n Biosample --|> TextValue : radiation_regm\n\n Biosample : rainfall_regm\n\n Biosample --|> TextValue : rainfall_regm\n\n Biosample : reactor_type\n\n Biosample --|> TextValue : reactor_type\n\n Biosample : redox_potential\n\n Biosample --|> QuantityValue : redox_potential\n\n Biosample : rel_air_humidity\n\n Biosample --|> QuantityValue : rel_air_humidity\n\n Biosample : rel_humidity_out\n\n Biosample --|> QuantityValue : rel_humidity_out\n\n Biosample : rel_samp_loc\n\n Biosample --|> rel_samp_loc_enum : rel_samp_loc\n\n Biosample : replicate_number\n\n Biosample : reservoir\n\n Biosample --|> TextValue : reservoir\n\n Biosample : resins_pc\n\n Biosample --|> TextValue : resins_pc\n\n Biosample : rna_absorb1\n\n Biosample : rna_absorb2\n\n Biosample : rna_collect_site\n\n Biosample : rna_concentration\n\n Biosample : rna_cont_type\n\n Biosample --|> JgiContTypeEnum : rna_cont_type\n\n Biosample : rna_cont_well\n\n Biosample : rna_container_id\n\n Biosample : rna_isolate_meth\n\n Biosample : rna_organisms\n\n Biosample : rna_project_contact\n\n Biosample : rna_samp_id\n\n Biosample : rna_sample_format\n\n Biosample --|> rna_sample_format_enum : rna_sample_format\n\n Biosample : rna_sample_name\n\n Biosample : rna_seq_project\n\n Biosample : rna_seq_project_name\n\n Biosample : rna_seq_project_pi\n\n Biosample : rna_volume\n\n Biosample : room_air_exch_rate\n\n Biosample --|> QuantityValue : room_air_exch_rate\n\n Biosample : room_architec_elem\n\n Biosample : room_condt\n\n Biosample --|> room_condt_enum : room_condt\n\n Biosample : room_connected\n\n Biosample --|> room_connected_enum : room_connected\n\n Biosample : room_count\n\n Biosample --|> TextValue : room_count\n\n Biosample : room_dim\n\n Biosample --|> TextValue : room_dim\n\n Biosample : room_door_dist\n\n Biosample --|> TextValue : room_door_dist\n\n Biosample : room_door_share\n\n Biosample --|> TextValue : room_door_share\n\n Biosample : room_hallway\n\n Biosample --|> TextValue : room_hallway\n\n Biosample : room_loc\n\n Biosample --|> room_loc_enum : room_loc\n\n Biosample : room_moist_dam_hist\n\n Biosample : room_net_area\n\n Biosample --|> TextValue : room_net_area\n\n Biosample : room_occup\n\n Biosample --|> QuantityValue : room_occup\n\n Biosample : room_samp_pos\n\n Biosample --|> room_samp_pos_enum : room_samp_pos\n\n Biosample : room_type\n\n Biosample --|> room_type_enum : room_type\n\n Biosample : room_vol\n\n Biosample --|> TextValue : room_vol\n\n Biosample : room_wall_share\n\n Biosample --|> TextValue : room_wall_share\n\n Biosample : room_window_count\n\n Biosample : root_cond\n\n Biosample --|> TextValue : root_cond\n\n Biosample : root_med_carbon\n\n Biosample --|> TextValue : root_med_carbon\n\n Biosample : root_med_macronutr\n\n Biosample --|> TextValue : root_med_macronutr\n\n Biosample : root_med_micronutr\n\n Biosample --|> TextValue : root_med_micronutr\n\n Biosample : root_med_ph\n\n Biosample --|> QuantityValue : root_med_ph\n\n Biosample : root_med_regl\n\n Biosample --|> TextValue : root_med_regl\n\n Biosample : root_med_solid\n\n Biosample --|> TextValue : root_med_solid\n\n Biosample : root_med_suppl\n\n Biosample --|> TextValue : root_med_suppl\n\n Biosample : salinity\n\n Biosample --|> QuantityValue : salinity\n\n Biosample : salinity_category\n\n Biosample : salinity_meth\n\n Biosample --|> TextValue : salinity_meth\n\n Biosample : salt_regm\n\n Biosample --|> TextValue : salt_regm\n\n Biosample : samp_capt_status\n\n Biosample --|> samp_capt_status_enum : samp_capt_status\n\n Biosample : samp_collec_device\n\n Biosample : samp_collec_method\n\n Biosample : samp_collect_point\n\n Biosample --|> samp_collect_point_enum : samp_collect_point\n\n Biosample : samp_dis_stage\n\n Biosample --|> samp_dis_stage_enum : samp_dis_stage\n\n Biosample : samp_floor\n\n Biosample --|> samp_floor_enum : samp_floor\n\n Biosample : samp_loc_corr_rate\n\n Biosample --|> TextValue : samp_loc_corr_rate\n\n Biosample : samp_mat_process\n\n Biosample --|> ControlledTermValue : samp_mat_process\n\n Biosample : samp_md\n\n Biosample --|> QuantityValue : samp_md\n\n Biosample : samp_name\n\n Biosample : samp_preserv\n\n Biosample --|> TextValue : samp_preserv\n\n Biosample : samp_room_id\n\n Biosample --|> TextValue : samp_room_id\n\n Biosample : samp_size\n\n Biosample --|> QuantityValue : samp_size\n\n Biosample : samp_sort_meth\n\n Biosample --|> TextValue : samp_sort_meth\n\n Biosample : samp_store_dur\n\n Biosample --|> TextValue : samp_store_dur\n\n Biosample : samp_store_loc\n\n Biosample --|> TextValue : samp_store_loc\n\n Biosample : samp_store_temp\n\n Biosample --|> QuantityValue : samp_store_temp\n\n Biosample : samp_subtype\n\n Biosample --|> samp_subtype_enum : samp_subtype\n\n Biosample : samp_taxon_id\n\n Biosample --|> ControlledIdentifiedTermValue : samp_taxon_id\n\n Biosample : samp_time_out\n\n Biosample --|> TextValue : samp_time_out\n\n Biosample : samp_transport_cond\n\n Biosample --|> TextValue : samp_transport_cond\n\n Biosample : samp_tvdss\n\n Biosample --|> TextValue : samp_tvdss\n\n Biosample : samp_type\n\n Biosample --|> TextValue : samp_type\n\n Biosample : samp_vol_we_dna_ext\n\n Biosample --|> QuantityValue : samp_vol_we_dna_ext\n\n Biosample : samp_weather\n\n Biosample --|> samp_weather_enum : samp_weather\n\n Biosample : samp_well_name\n\n Biosample --|> TextValue : samp_well_name\n\n Biosample : sample_collection_site\n\n Biosample : sample_link\n\n Biosample : sample_shipped\n\n Biosample : sample_type\n\n Biosample --|> sample_type_enum : sample_type\n\n Biosample : saturates_pc\n\n Biosample --|> TextValue : saturates_pc\n\n Biosample : season\n\n Biosample --|> TextValue : season\n\n Biosample : season_environment\n\n Biosample --|> TextValue : season_environment\n\n Biosample : season_precpt\n\n Biosample --|> QuantityValue : season_precpt\n\n Biosample : season_temp\n\n Biosample --|> QuantityValue : season_temp\n\n Biosample : season_use\n\n Biosample --|> season_use_enum : season_use\n\n Biosample : secondary_treatment\n\n Biosample --|> TextValue : secondary_treatment\n\n Biosample : sediment_type\n\n Biosample --|> sediment_type_enum : sediment_type\n\n Biosample : seq_meth\n\n Biosample --|> TextValue : seq_meth\n\n Biosample : seq_quality_check\n\n Biosample --|> TextValue : seq_quality_check\n\n Biosample : sequencing_field\n\n Biosample : sewage_type\n\n Biosample --|> TextValue : sewage_type\n\n Biosample : shad_dev_water_mold\n\n Biosample : shading_device_cond\n\n Biosample --|> shading_device_cond_enum : shading_device_cond\n\n Biosample : shading_device_loc\n\n Biosample --|> TextValue : shading_device_loc\n\n Biosample : shading_device_mat\n\n Biosample --|> TextValue : shading_device_mat\n\n Biosample : shading_device_type\n\n Biosample --|> shading_device_type_enum : shading_device_type\n\n Biosample : sieving\n\n Biosample --|> TextValue : sieving\n\n Biosample : silicate\n\n Biosample --|> QuantityValue : silicate\n\n Biosample : size_frac\n\n Biosample --|> TextValue : size_frac\n\n Biosample : size_frac_low\n\n Biosample --|> QuantityValue : size_frac_low\n\n Biosample : size_frac_up\n\n Biosample --|> QuantityValue : size_frac_up\n\n Biosample : slope_aspect\n\n Biosample --|> QuantityValue : slope_aspect\n\n Biosample : slope_gradient\n\n Biosample --|> QuantityValue : slope_gradient\n\n Biosample : sludge_retent_time\n\n Biosample --|> QuantityValue : sludge_retent_time\n\n Biosample : sodium\n\n Biosample --|> QuantityValue : sodium\n\n Biosample : soil_horizon\n\n Biosample --|> soil_horizon_enum : soil_horizon\n\n Biosample : soil_text_measure\n\n Biosample --|> QuantityValue : soil_text_measure\n\n Biosample : soil_texture_meth\n\n Biosample : soil_type\n\n Biosample --|> TextValue : soil_type\n\n Biosample : soil_type_meth\n\n Biosample --|> TextValue : soil_type_meth\n\n Biosample : solar_irradiance\n\n Biosample --|> QuantityValue : solar_irradiance\n\n Biosample : soluble_inorg_mat\n\n Biosample --|> TextValue : soluble_inorg_mat\n\n Biosample : soluble_iron_micromol\n\n Biosample : soluble_org_mat\n\n Biosample --|> TextValue : soluble_org_mat\n\n Biosample : soluble_react_phosp\n\n Biosample --|> QuantityValue : soluble_react_phosp\n\n Biosample : source_mat_id\n\n Biosample --|> TextValue : source_mat_id\n\n Biosample : space_typ_state\n\n Biosample --|> TextValue : space_typ_state\n\n Biosample : specific\n\n Biosample --|> specific_enum : specific\n\n Biosample : specific_ecosystem\n\n Biosample : specific_humidity\n\n Biosample --|> QuantityValue : specific_humidity\n\n Biosample : sr_dep_env\n\n Biosample --|> sr_dep_env_enum : sr_dep_env\n\n Biosample : sr_geol_age\n\n Biosample --|> sr_geol_age_enum : sr_geol_age\n\n Biosample : sr_kerog_type\n\n Biosample --|> sr_kerog_type_enum : sr_kerog_type\n\n Biosample : sr_lithology\n\n Biosample --|> sr_lithology_enum : sr_lithology\n\n Biosample : standing_water_regm\n\n Biosample --|> TextValue : standing_water_regm\n\n Biosample : start_date_inc\n\n Biosample : start_time_inc\n\n Biosample : store_cond\n\n Biosample --|> TextValue : store_cond\n\n Biosample : substructure_type\n\n Biosample --|> substructure_type_enum : substructure_type\n\n Biosample : subsurface_depth\n\n Biosample --|> QuantityValue : subsurface_depth\n\n Biosample : sulfate\n\n Biosample --|> QuantityValue : sulfate\n\n Biosample : sulfate_fw\n\n Biosample --|> QuantityValue : sulfate_fw\n\n Biosample : sulfide\n\n Biosample --|> QuantityValue : sulfide\n\n Biosample : surf_air_cont\n\n Biosample --|> surf_air_cont_enum : surf_air_cont\n\n Biosample : surf_humidity\n\n Biosample --|> QuantityValue : surf_humidity\n\n Biosample : surf_material\n\n Biosample --|> surf_material_enum : surf_material\n\n Biosample : surf_moisture\n\n Biosample --|> QuantityValue : surf_moisture\n\n Biosample : surf_moisture_ph\n\n Biosample : surf_temp\n\n Biosample --|> QuantityValue : surf_temp\n\n Biosample : suspend_part_matter\n\n Biosample --|> QuantityValue : suspend_part_matter\n\n Biosample : suspend_solids\n\n Biosample --|> TextValue : suspend_solids\n\n Biosample : tan\n\n Biosample --|> QuantityValue : tan\n\n Biosample : target_gene\n\n Biosample --|> TextValue : target_gene\n\n Biosample : target_subfragment\n\n Biosample --|> TextValue : target_subfragment\n\n Biosample : technical_reps\n\n Biosample : temp\n\n Biosample --|> QuantityValue : temp\n\n Biosample : temp_out\n\n Biosample --|> QuantityValue : temp_out\n\n Biosample : tertiary_treatment\n\n Biosample --|> TextValue : tertiary_treatment\n\n Biosample : tidal_stage\n\n Biosample --|> tidal_stage_enum : tidal_stage\n\n Biosample : tillage\n\n Biosample --|> tillage_enum : tillage\n\n Biosample : tiss_cult_growth_med\n\n Biosample --|> TextValue : tiss_cult_growth_med\n\n Biosample : toluene\n\n Biosample --|> QuantityValue : toluene\n\n Biosample : tot_carb\n\n Biosample --|> QuantityValue : tot_carb\n\n Biosample : tot_depth_water_col\n\n Biosample --|> QuantityValue : tot_depth_water_col\n\n Biosample : tot_diss_nitro\n\n Biosample --|> QuantityValue : tot_diss_nitro\n\n Biosample : tot_inorg_nitro\n\n Biosample --|> QuantityValue : tot_inorg_nitro\n\n Biosample : tot_iron\n\n Biosample --|> QuantityValue : tot_iron\n\n Biosample : tot_nitro\n\n Biosample --|> QuantityValue : tot_nitro\n\n Biosample : tot_nitro_cont_meth\n\n Biosample : tot_nitro_content\n\n Biosample --|> QuantityValue : tot_nitro_content\n\n Biosample : tot_org_c_meth\n\n Biosample --|> TextValue : tot_org_c_meth\n\n Biosample : tot_org_carb\n\n Biosample --|> QuantityValue : tot_org_carb\n\n Biosample : tot_part_carb\n\n Biosample --|> QuantityValue : tot_part_carb\n\n Biosample : tot_phosp\n\n Biosample --|> QuantityValue : tot_phosp\n\n Biosample : tot_phosphate\n\n Biosample --|> QuantityValue : tot_phosphate\n\n Biosample : tot_sulfur\n\n Biosample --|> QuantityValue : tot_sulfur\n\n Biosample : train_line\n\n Biosample --|> train_line_enum : train_line\n\n Biosample : train_stat_loc\n\n Biosample --|> train_stat_loc_enum : train_stat_loc\n\n Biosample : train_stop_loc\n\n Biosample --|> train_stop_loc_enum : train_stop_loc\n\n Biosample : turbidity\n\n Biosample --|> QuantityValue : turbidity\n\n Biosample : tvdss_of_hcr_press\n\n Biosample --|> QuantityValue : tvdss_of_hcr_press\n\n Biosample : tvdss_of_hcr_temp\n\n Biosample --|> QuantityValue : tvdss_of_hcr_temp\n\n Biosample : typ_occup_density\n\n Biosample : type\n\n Biosample : ventilation_rate\n\n Biosample --|> QuantityValue : ventilation_rate\n\n Biosample : ventilation_type\n\n Biosample --|> TextValue : ventilation_type\n\n Biosample : vfa\n\n Biosample --|> QuantityValue : vfa\n\n Biosample : vfa_fw\n\n Biosample --|> QuantityValue : vfa_fw\n\n Biosample : vis_media\n\n Biosample --|> vis_media_enum : vis_media\n\n Biosample : viscosity\n\n Biosample --|> TextValue : viscosity\n\n Biosample : volatile_org_comp\n\n Biosample --|> TextValue : volatile_org_comp\n\n Biosample : wall_area\n\n Biosample --|> QuantityValue : wall_area\n\n Biosample : wall_const_type\n\n Biosample --|> wall_const_type_enum : wall_const_type\n\n Biosample : wall_finish_mat\n\n Biosample --|> wall_finish_mat_enum : wall_finish_mat\n\n Biosample : wall_height\n\n Biosample --|> QuantityValue : wall_height\n\n Biosample : wall_loc\n\n Biosample --|> wall_loc_enum : wall_loc\n\n Biosample : wall_surf_treatment\n\n Biosample --|> wall_surf_treatment_enum : wall_surf_treatment\n\n Biosample : wall_texture\n\n Biosample --|> wall_texture_enum : wall_texture\n\n Biosample : wall_thermal_mass\n\n Biosample --|> QuantityValue : wall_thermal_mass\n\n Biosample : wall_water_mold\n\n Biosample --|> TextValue : wall_water_mold\n\n Biosample : wastewater_type\n\n Biosample --|> TextValue : wastewater_type\n\n Biosample : water_cont_soil_meth\n\n Biosample : water_content\n\n Biosample : water_current\n\n Biosample --|> QuantityValue : water_current\n\n Biosample : water_cut\n\n Biosample --|> QuantityValue : water_cut\n\n Biosample : water_feat_size\n\n Biosample --|> QuantityValue : water_feat_size\n\n Biosample : water_feat_type\n\n Biosample --|> water_feat_type_enum : water_feat_type\n\n Biosample : water_prod_rate\n\n Biosample --|> QuantityValue : water_prod_rate\n\n Biosample : water_temp_regm\n\n Biosample --|> TextValue : water_temp_regm\n\n Biosample : watering_regm\n\n Biosample --|> TextValue : watering_regm\n\n Biosample : weekday\n\n Biosample --|> weekday_enum : weekday\n\n Biosample : win\n\n Biosample --|> TextValue : win\n\n Biosample : wind_direction\n\n Biosample --|> TextValue : wind_direction\n\n Biosample : wind_speed\n\n Biosample --|> QuantityValue : wind_speed\n\n Biosample : window_cond\n\n Biosample --|> window_cond_enum : window_cond\n\n Biosample : window_cover\n\n Biosample --|> window_cover_enum : window_cover\n\n Biosample : window_horiz_pos\n\n Biosample --|> window_horiz_pos_enum : window_horiz_pos\n\n Biosample : window_loc\n\n Biosample --|> window_loc_enum : window_loc\n\n Biosample : window_mat\n\n Biosample --|> window_mat_enum : window_mat\n\n Biosample : window_open_freq\n\n Biosample --|> TextValue : window_open_freq\n\n Biosample : window_size\n\n Biosample --|> TextValue : window_size\n\n Biosample : window_status\n\n Biosample --|> TextValue : window_status\n\n Biosample : window_type\n\n Biosample --|> window_type_enum : window_type\n\n Biosample : window_vert_pos\n\n Biosample --|> window_vert_pos_enum : window_vert_pos\n\n Biosample : window_water_mold\n\n Biosample --|> TextValue : window_water_mold\n\n Biosample : xylene\n\n Biosample --|> QuantityValue : xylene\n\n Biosample : zinc\n\n Biosample --|> QuantityValue : zinc\n\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\ntodos:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslots:\n- neon_biosample_identifiers\n- host_taxid\n- embargoed\n- collected_from\n- type\n- img_identifiers\n- samp_name\n- biosample_categories\n- type\n- part_of\n- id\n- alternative_identifiers\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chimera_check\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- has numeric value\n- has raw value\n- has unit\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucl_acid_amp\n- nucl_acid_ext\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- pcr_cond\n- pcr_primers\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- pool_dna_extracts\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_vol_we_dna_ext\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- seq_meth\n- seq_quality_check\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- target_gene\n- target_subfragment\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n oxy_stat_samp:\n name: oxy_stat_samp\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n domain_of:\n - Biosample\n range: uriorcurie\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n lat_lon:\n name: lat_lon\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n domain_of:\n - FieldResearchSite\n - Biosample\n env_broad_scale:\n name: env_broad_scale\n domain_of:\n - Biosample\n required: true\n env_local_scale:\n name: env_local_scale\n domain_of:\n - Biosample\n required: true\n env_medium:\n name: env_medium\n domain_of:\n - Biosample\n required: true\n part_of:\n name: part_of\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n domain_of:\n - Biosample\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n domain_of:\n - Biosample\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n domain_of:\n - Biosample\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n domain_of:\n - Biosample\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n domain_of:\n - Biosample\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n domain_of:\n - Biosample\n annual_precpt:\n name: annual_precpt\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n domain_of:\n - Biosample\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n domain_of:\n - FieldResearchSite\n - Biosample\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n domain_of:\n - Biosample\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n domain_of:\n - Biosample\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n domain_of:\n - Biosample\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n domain_of:\n - Biosample\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n domain_of:\n - Biosample\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n multivalued: true\n domain_of:\n - Biosample\n range: string\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n domain_of:\n - Biosample\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n domain_of:\n - Biosample\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n domain_of:\n - Biosample\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n domain_of:\n - Biosample\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n domain_of:\n - Biosample\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n domain_of:\n - Biosample\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n domain_of:\n - Biosample\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n domain_of:\n - Biosample\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n domain_of:\n - Biosample\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n domain_of:\n - Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\n notes:\n - 'id is already required to be unique because it is the identifier in Biosample''s\n parent class, NamedThing. Remember, notes like this could be exposed to end\n users. CJM suggested YAML # comment'\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\ntodos:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslot_usage:\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n oxy_stat_samp:\n name: oxy_stat_samp\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n domain_of:\n - Biosample\n range: uriorcurie\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n lat_lon:\n name: lat_lon\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n domain_of:\n - FieldResearchSite\n - Biosample\n env_broad_scale:\n name: env_broad_scale\n domain_of:\n - Biosample\n required: true\n env_local_scale:\n name: env_local_scale\n domain_of:\n - Biosample\n required: true\n env_medium:\n name: env_medium\n domain_of:\n - Biosample\n required: true\n part_of:\n name: part_of\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n domain_of:\n - Biosample\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n domain_of:\n - Biosample\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n domain_of:\n - Biosample\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n domain_of:\n - Biosample\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n domain_of:\n - Biosample\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n domain_of:\n - Biosample\n annual_precpt:\n name: annual_precpt\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n domain_of:\n - Biosample\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n domain_of:\n - FieldResearchSite\n - Biosample\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n domain_of:\n - Biosample\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n domain_of:\n - Biosample\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n domain_of:\n - Biosample\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n domain_of:\n - Biosample\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n domain_of:\n - Biosample\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n multivalued: true\n domain_of:\n - Biosample\n range: string\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n domain_of:\n - Biosample\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n domain_of:\n - Biosample\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n domain_of:\n - Biosample\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n domain_of:\n - Biosample\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n domain_of:\n - Biosample\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n domain_of:\n - Biosample\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n domain_of:\n - Biosample\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n domain_of:\n - Biosample\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n domain_of:\n - Biosample\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n domain_of:\n - Biosample\nattributes:\n neon_biosample_identifiers:\n name: neon_biosample_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - neon_identifiers\n multivalued: true\n alias: neon_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n host_taxid:\n name: host_taxid\n annotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: NCBI taxon id of the host, e.g. 9606\n title: host taxid\n comments:\n - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host taxid\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000250\n multivalued: false\n alias: host_taxid\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n embargoed:\n name: embargoed\n description: If true, the data are embargoed and not available for public access.\n todos:\n - make this required?\n - first apply to Biosample\n - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n - applying to a Study may nto be granular enough\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: embargoed\n owner: Biosample\n domain_of:\n - Biosample\n range: boolean\n recommended: true\n collected_from:\n name: collected_from\n description: The Site from which a Biosample was collected\n todos:\n - add an OBO slot_uri ?\n comments:\n - this illustrates implementing a Biosample relation with a (binary) slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Biosample\n alias: collected_from\n owner: Biosample\n domain_of:\n - Biosample\n range: FieldResearchSite\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: Biosample\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n multivalued: true\n alias: img_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n samp_name:\n name: samp_name\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A local identifier or name that for the material sample used for\n extracting nucleic acids, and subsequent sequencing. It can refer either to\n the original material collected or to any derived sub-samples. It can have any\n format, but we suggest that you make it concise, unique and consistent within\n your lab, and as informative as possible. INSDC requires every sample name from\n a single Submitter to be unique. Use of a globally unique identifier for the\n field source_mat_id is recommended in addition to sample_name.\n title: sample name\n examples:\n - value: ISDsoil1\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample name\n rank: 1000\n is_a: investigation field\n string_serialization: '{text}'\n slot_uri: MIXS:0001107\n multivalued: false\n alias: samp_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n biosample_categories:\n name: biosample_categories\n title: Categories the biosample belongs to\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: biosample_categories\n owner: Biosample\n domain_of:\n - Biosample\n range: BiosampleCategoryEnum\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n multivalued: true\n alias: gold_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: uriorcurie\n pattern: ^gold:Gb[0-9]+$\n insdc_biosample_identifiers:\n name: insdc_biosample_identifiers\n description: identifiers for corresponding sample in INSDC\n examples:\n - value: https://bioregistry.io/biosample:SAMEA5989477\n - value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational\n gradients\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/bioregistry/bioregistry/issues/108\n - https://www.ebi.ac.uk/biosamples/\n - https://www.ncbi.nlm.nih.gov/biosample\n - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n aliases:\n - EBI biosample identifiers\n - NCBI biosample identifiers\n - DDBJ biosample identifiers\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - insdc_identifiers\n multivalued: true\n alias: insdc_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n emsl_biosample_identifiers:\n name: emsl_biosample_identifiers\n description: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\n title: EMSL Biosample Identifiers\n todos:\n - removed \"planned\" once NEXUS is online\n - determine real expansion for emsl prefix\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - emsl_identifiers\n multivalued: true\n alias: emsl_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n igsn_biosample_identifiers:\n name: igsn_biosample_identifiers\n description: A list of identifiers for the biosample from the IGSN database.\n title: IGSN Biosample Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - igsn_identifiers\n multivalued: true\n alias: igsn_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n abs_air_humidity:\n name: abs_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\n description: Actual mass of water vapor - mh20 - present in the air water vapor\n mixture\n title: absolute air humidity\n examples:\n - value: 9 gram per gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - absolute air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000122\n multivalued: false\n alias: abs_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_recov_method:\n name: add_recov_method\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one\n of them. If \"other\" is specified, please propose entry in \"additional info\"\n field\n title: secondary and tertiary recovery methods and start date\n examples:\n - value: Polymer Addition;2018-06-21T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary and tertiary recovery methods and start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001009\n multivalued: false\n alias: add_recov_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n additional_info:\n name: additional_info\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\n title: additional info\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - additional info\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000300\n multivalued: false\n alias: additional_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n address:\n name: address\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The street name and building number where the sampling occurred.\n title: address\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - address\n rank: 1000\n is_a: core field\n string_serialization: '{integer}{text}'\n slot_uri: MIXS:0000218\n multivalued: false\n alias: address\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n adj_room:\n name: adj_room\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms (room number, room name) immediately adjacent to the\n sampling room\n title: adjacent rooms\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - adjacent rooms\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000219\n multivalued: false\n alias: adj_room\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n aero_struc:\n name: aero_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\n title: aerospace structure\n examples:\n - value: plane\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aerospace structure\n rank: 1000\n is_a: core field\n string_serialization: '[plane|glider]'\n slot_uri: MIXS:0000773\n multivalued: false\n alias: aero_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n agrochem_addition:\n name: agrochem_addition\n annotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n title: history/agrochemical additions\n examples:\n - value: roundup;5 milligram per liter;2018-06-21\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/agrochemical additions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{timestamp}'\n slot_uri: MIXS:0000639\n multivalued: true\n alias: agrochem_addition\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n air_PM_concen:\n name: air_PM_concen\n annotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances that remain suspended in the air, and\n comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n report multiple PM's by entering numeric values preceded by name of PM\n title: air particulate matter concentration\n examples:\n - value: PM2.5;10 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air particulate matter concentration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000108\n multivalued: true\n alias: air_PM_concen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n air_temp:\n name: air_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the air at the time of sampling\n title: air temperature\n examples:\n - value: 20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000124\n multivalued: false\n alias: air_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n air_temp_regm:\n name: air_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include different temperature regimens\n title: air temperature regimen\n examples:\n - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000551\n multivalued: true\n alias: air_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000607\n multivalued: false\n alias: al_sat\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000324\n multivalued: false\n alias: al_sat_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n alkalinity:\n name: alkalinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Alkalinity, the ability of a solution to neutralize acids to the\n equivalence point of carbonate or bicarbonate\n title: alkalinity\n examples:\n - value: 50 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000421\n multivalued: false\n alias: alkalinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n alkalinity_method:\n name: alkalinity_method\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\n description: Method used for alkalinity measurement\n title: alkalinity method\n examples:\n - value: titration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000298\n multivalued: false\n alias: alkalinity_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n alkyl_diethers:\n name: alkyl_diethers\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of alkyl diethers\n title: alkyl diethers\n examples:\n - value: 0.005 mole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkyl diethers\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000490\n multivalued: false\n alias: alkyl_diethers\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n alt:\n name: alt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as\n atmospheric layers and clouds. It is used to measure the height of an object\n which is above the earth's surface. In this context, the altitude measurement\n is the vertical distance between the earth's surface above sea level and the\n sampled position in the air\n title: altitude\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - altitude\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000094\n multivalued: false\n alias: alt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n aminopept_act:\n name: aminopept_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of aminopeptidase activity\n title: aminopeptidase activity\n examples:\n - value: 0.269 mole per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aminopeptidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000172\n multivalued: false\n alias: aminopept_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ammonium:\n name: ammonium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium in the sample\n title: ammonium\n examples:\n - value: 1.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ammonium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000427\n multivalued: false\n alias: ammonium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ammonium_nitrogen:\n name: ammonium_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium nitrogen in the sample\n title: ammonium nitrogen\n examples:\n - value: 2.3 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - ammonium_nitrogen\n - NH4-N\n rank: 1000\n is_a: attribute\n alias: ammonium_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n amount_light:\n name: amount_light\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The unit of illuminance and luminous emittance, measuring luminous\n flux per unit area\n title: amount of light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount of light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000140\n multivalued: false\n alias: amount_light\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ances_data:\n name: ances_data\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about either pedigree or other ancestral information\n description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n (meaning [(A x B) x B] x B)\n title: ancestral data\n examples:\n - value: A/3*B\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ancestral data\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000247\n multivalued: false\n alias: ances_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n annual_precpt:\n name: annual_precpt\n description: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: mean annual precipitation\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000644\n multivalued: false\n alias: annual_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n annual_temp:\n name: annual_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean annual temperature\n title: mean annual temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000642\n multivalued: false\n alias: annual_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n antibiotic_regm:\n name: antibiotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving antibiotic administration;\n should include the name of antibiotic, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n antibiotic regimens\n title: antibiotic regimen\n examples:\n - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - antibiotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000553\n multivalued: true\n alias: antibiotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n api:\n name: api\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\n description: 'API gravity is a measure of how heavy or light a petroleum liquid\n is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n 31.1\u00ac\u221e API)'\n title: API gravity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - API gravity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000157\n multivalued: false\n alias: api\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n arch_struc:\n name: arch_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: An architectural structure is a human-made, free-standing, immobile\n outdoor construction\n title: architectural structure\n examples:\n - value: shed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - architectural structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000774\n multivalued: false\n alias: arch_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: arch_struc_enum\n aromatics_pc:\n name: aromatics_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: aromatics wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aromatics wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000133\n multivalued: false\n alias: aromatics_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n asphaltenes_pc:\n name: asphaltenes_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: asphaltenes wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - asphaltenes wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000135\n multivalued: false\n alias: asphaltenes_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n atmospheric_data:\n name: atmospheric_data\n annotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Measurement of atmospheric data; can include multiple data\n title: atmospheric data\n examples:\n - value: wind speed;9 knots\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - atmospheric data\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0001097\n multivalued: true\n alias: atmospheric_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n avg_dew_point:\n name: avg_dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of dew point measures taken at the beginning of every\n hour over a 24 hour period on the sampling day\n title: average dew point\n examples:\n - value: 25.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000141\n multivalued: false\n alias: avg_dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n avg_occup:\n name: avg_occup\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Daily average occupancy of room. Indicate the number of person(s)\n daily occupying the sampling room.\n title: average daily occupancy\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average daily occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000775\n multivalued: false\n alias: avg_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n avg_temp:\n name: avg_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of temperatures taken at the beginning of every hour\n over a 24 hour period on the sampling day\n title: average temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000142\n multivalued: false\n alias: avg_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bac_prod:\n name: bac_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Bacterial production in the water column measured by isotope uptake\n title: bacterial production\n examples:\n - value: 5 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000683\n multivalued: false\n alias: bac_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bac_resp:\n name: bac_resp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial respiration in the water column\n title: bacterial respiration\n examples:\n - value: 300 micromole oxygen per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial respiration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000684\n multivalued: false\n alias: bac_resp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bacteria_carb_prod:\n name: bacteria_carb_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial carbon production\n title: bacterial carbon production\n examples:\n - value: 2.53 microgram per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial carbon production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000173\n multivalued: false\n alias: bacteria_carb_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n barometric_press:\n name: barometric_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\n description: Force per unit area exerted against a surface by the weight of air\n above that surface\n title: barometric pressure\n examples:\n - value: 5 millibar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - barometric pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000096\n multivalued: false\n alias: barometric_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n basin:\n name: basin\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the basin (e.g. Campos)\n title: basin name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - basin name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000290\n multivalued: false\n alias: basin\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n bathroom_count:\n name: bathroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bathrooms in the building\n title: bathroom count\n examples:\n - value: '1'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bathroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000776\n multivalued: false\n alias: bathroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n bedroom_count:\n name: bedroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bedrooms in the building\n title: bedroom count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bedroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000777\n multivalued: false\n alias: bedroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n benzene:\n name: benzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of benzene in the sample\n title: benzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - benzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000153\n multivalued: false\n alias: benzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n biochem_oxygen_dem:\n name: biochem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of dissolved oxygen needed by aerobic biological organisms\n in a body of water to break down organic material present in a given water sample\n at certain temperature over a specific time period\n title: biochemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biochemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000653\n multivalued: false\n alias: biochem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n biocide:\n name: biocide\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of biocides (commercial name of product and supplier) and date\n of administration\n title: biocide administration\n examples:\n - value: ALPHA 1427;Baker Hughes;2008-01-23\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001011\n multivalued: false\n alias: biocide\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biocide_admin_method:\n name: biocide_admin_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of biocide administration (dose, frequency, duration, time\n elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n days)\n title: biocide administration method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n slot_uri: MIXS:0000456\n multivalued: false\n alias: biocide_admin_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biol_stat:\n name: biol_stat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The level of genome modification.\n title: biological status\n examples:\n - value: natural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biological status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000858\n multivalued: false\n alias: biol_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: biol_stat_enum\n biomass:\n name: biomass\n annotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g. Microbial, total. Can include multiple measurements\n title: biomass\n examples:\n - value: total;20 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biomass\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000174\n multivalued: true\n alias: biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biotic_regm:\n name: biotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\n title: biotic regimen\n examples:\n - value: sample inoculated with Rhizobium spp. Culture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001038\n multivalued: false\n alias: biotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biotic_relationship:\n name: biotic_relationship\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n description: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with\n species Y. The target organism is the subject of the relationship, and the other\n organism(s) is the object\n title: observed biotic relationship\n examples:\n - value: free living\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed biotic relationship\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000028\n multivalued: false\n alias: biotic_relationship\n owner: Biosample\n domain_of:\n - Biosample\n range: biotic_relationship_enum\n bishomohopanol:\n name: bishomohopanol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bishomohopanol\n title: bishomohopanol\n examples:\n - value: 14 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bishomohopanol\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000175\n multivalued: false\n alias: bishomohopanol\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n blood_press_diast:\n name: blood_press_diast\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting diastolic blood pressure, measured as mm mercury\n title: host blood pressure diastolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure diastolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000258\n multivalued: false\n alias: blood_press_diast\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n blood_press_syst:\n name: blood_press_syst\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting systolic blood pressure, measured as mm mercury\n title: host blood pressure systolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure systolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000259\n multivalued: false\n alias: blood_press_syst\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bromide:\n name: bromide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bromide\n title: bromide\n examples:\n - value: 0.05 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bromide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000176\n multivalued: false\n alias: bromide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n build_docs:\n name: build_docs\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building design, construction and operation documents\n title: design, construction, and operation documents\n examples:\n - value: maintenance plans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - design, construction, and operation documents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000787\n multivalued: false\n alias: build_docs\n owner: Biosample\n domain_of:\n - Biosample\n range: build_docs_enum\n build_occup_type:\n name: build_occup_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The primary function for which a building or discrete part of a building\n is intended to be used\n title: building occupancy type\n examples:\n - value: market\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building occupancy type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000761\n multivalued: true\n alias: build_occup_type\n owner: Biosample\n domain_of:\n - Biosample\n range: build_occup_type_enum\n building_setting:\n name: building_setting\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A location (geography) where a building is set\n title: building setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building setting\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000768\n multivalued: false\n alias: building_setting\n owner: Biosample\n domain_of:\n - Biosample\n range: building_setting_enum\n built_struc_age:\n name: built_struc_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\n description: The age of the built structure since construction\n title: built structure age\n examples:\n - value: '15'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000145\n multivalued: false\n alias: built_struc_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n built_struc_set:\n name: built_struc_set\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The characterization of the location of the built structure as high\n or low human density\n title: built structure setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure setting\n rank: 1000\n is_a: core field\n string_serialization: '[urban|rural]'\n slot_uri: MIXS:0000778\n multivalued: false\n alias: built_struc_set\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n built_struc_type:\n name: built_struc_type\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\n title: built structure type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000721\n multivalued: false\n alias: built_struc_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n calcium:\n name: calcium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of calcium in the sample\n title: calcium\n examples:\n - value: 0.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - calcium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000432\n multivalued: false\n alias: calcium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_dioxide:\n name: carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon dioxide (gas) amount or concentration at the time of sampling\n title: carbon dioxide\n examples:\n - value: 410 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000097\n multivalued: false\n alias: carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_monoxide:\n name: carb_monoxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon monoxide (gas) amount or concentration at the time of sampling\n title: carbon monoxide\n examples:\n - value: 0.1 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon monoxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000098\n multivalued: false\n alias: carb_monoxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_nitro_ratio:\n name: carb_nitro_ratio\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ratio of amount or concentrations of carbon to nitrogen\n title: carbon/nitrogen ratio\n examples:\n - value: '0.417361111'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon/nitrogen ratio\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000310\n multivalued: false\n alias: carb_nitro_ratio\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_area:\n name: ceil_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the ceiling space within the room\n title: ceiling area\n examples:\n - value: 25 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000148\n multivalued: false\n alias: ceil_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_cond:\n name: ceil_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: ceiling condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000779\n multivalued: false\n alias: ceil_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_cond_enum\n ceil_finish_mat:\n name: ceil_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a ceiling\n title: ceiling finish material\n examples:\n - value: stucco\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000780\n multivalued: false\n alias: ceil_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_finish_mat_enum\n ceil_struc:\n name: ceil_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The construction format of the ceiling\n title: ceiling structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling structure\n rank: 1000\n is_a: core field\n string_serialization: '[wood frame|concrete]'\n slot_uri: MIXS:0000782\n multivalued: false\n alias: ceil_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ceil_texture:\n name: ceil_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a ceiling surface\n title: ceiling texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000783\n multivalued: false\n alias: ceil_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_texture_enum\n ceil_thermal_mass:\n name: ceil_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the ceiling to provide inertia against temperature\n fluctuations. Generally this means concrete that is exposed. A metal deck that\n supports a concrete slab will act thermally as long as it is exposed to room\n air flow\n title: ceiling thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000143\n multivalued: false\n alias: ceil_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_type:\n name: ceil_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of ceiling according to the ceiling's appearance or construction\n title: ceiling type\n examples:\n - value: coffered\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000784\n multivalued: false\n alias: ceil_type\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_type_enum\n ceil_water_mold:\n name: ceil_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the ceiling\n title: ceiling signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000781\n multivalued: false\n alias: ceil_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chem_administration:\n name: chem_administration\n annotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\n description: List of chemical compounds administered to the host or site where\n sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n include multiple compounds. For chemical entities of biological interest ontology\n (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n title: chemical administration\n examples:\n - value: agar [CHEBI:2509];2018-05-11T20:00Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical administration\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]};{timestamp}'\n slot_uri: MIXS:0000751\n multivalued: true\n alias: chem_administration\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n chem_mutagen:\n name: chem_mutagen\n annotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple mutagen regimens\n title: chemical mutagen\n examples:\n - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical mutagen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000555\n multivalued: true\n alias: chem_mutagen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chem_oxygen_dem:\n name: chem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and\n nitrite\n title: chemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000656\n multivalued: false\n alias: chem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n chem_treat_method:\n name: chem_treat_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of chemical administration(dose, frequency, duration, time\n elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n hr; 0 days)\n title: chemical treatment method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n slot_uri: MIXS:0000457\n multivalued: false\n alias: chem_treat_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n chem_treatment:\n name: chem_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the\n product and name of the supplier should be provided. The date of administration\n should also be included\n title: chemical treatment\n examples:\n - value: ACCENT 1125;DOW;2010-11-17\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001012\n multivalued: false\n alias: chem_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chimera_check:\n name: chimera_check\n annotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\n description: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised\n of two or more phylogenetically distinct parent sequences.\n title: chimera check software\n examples:\n - value: uchime;v4.1;default parameters\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chimera check software\n rank: 1000\n is_a: sequencing field\n string_serialization: '{software};{version};{parameters}'\n slot_uri: MIXS:0000052\n multivalued: false\n alias: chimera_check\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n chloride:\n name: chloride\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chloride in the sample\n title: chloride\n examples:\n - value: 5000 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chloride\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000429\n multivalued: false\n alias: chloride\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n chlorophyll:\n name: chlorophyll\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chlorophyll\n title: chlorophyll\n examples:\n - value: 5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chlorophyll\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000177\n multivalued: false\n alias: chlorophyll\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n climate_environment:\n name: climate_environment\n description: Treatment involving an exposure to a particular climate; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n climates\n title: climate environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001040\n multivalued: true\n alias: climate_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n collection_date:\n name: collection_date\n annotations:\n expected_value:\n tag: expected_value\n value: date and time\n description: 'The time of sampling, either as an instance (single point in time)\n or interval. In case no exact time is available, the date/time can be right\n truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n title: collection date\n examples:\n - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - collection date\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000011\n multivalued: false\n alias: collection_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n conduc:\n name: conduc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Electrical conductivity of water\n title: conductivity\n examples:\n - value: 10 milliSiemens per centimeter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - conductivity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000692\n multivalued: false\n alias: conduc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n cool_syst_id:\n name: cool_syst_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The cooling system identifier\n title: cooling system identifier\n examples:\n - value: '12345'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - cooling system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000785\n multivalued: false\n alias: cool_syst_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n core field:\n name: core field\n description: basic fields\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: core_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n crop_rotation:\n name: crop_rotation\n annotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not crop is rotated, and if yes, rotation schedule\n title: history/crop rotation\n examples:\n - value: yes;R2/2017-01-01/2018-12-31/P6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/crop rotation\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000318\n multivalued: false\n alias: crop_rotation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n cult_root_med:\n name: cult_root_med\n annotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Name or reference for the hydroponic or in vitro culture rooting\n medium; can be the name of a commonly used medium or reference to a specific\n medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n published, use the rooting medium descriptors.\n title: culture rooting medium\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - culture rooting medium\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001041\n multivalued: false\n alias: cult_root_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n cur_land_use:\n name: cur_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Present state of sample site\n title: current land use\n examples:\n - value: conifers\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current land use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001080\n multivalued: false\n alias: cur_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: cur_land_use_enum\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n multivalued: false\n alias: cur_vegetation\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n cur_vegetation_meth:\n name: cur_vegetation_meth\n description: Reference or method used in vegetation classification\n title: current vegetation method\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000314\n multivalued: false\n alias: cur_vegetation_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n date_last_rain:\n name: date_last_rain\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The date of the last time it rained\n title: date last rain\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - date last rain\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000786\n multivalued: false\n alias: date_last_rain\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n density:\n name: density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\n title: density\n examples:\n - value: 1000 kilogram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000435\n multivalued: false\n alias: density\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n depos_env:\n name: depos_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: depositional environment\n examples:\n - value: Continental - Alluvial\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000992\n multivalued: false\n alias: depos_env\n owner: Biosample\n domain_of:\n - Biosample\n range: depos_env_enum\n depth:\n name: depth\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth\n can be reported as an interval for subsurface samples.\n title: depth\n examples:\n - value: 10 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000018\n multivalued: false\n alias: depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dew_point:\n name: dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\n title: dew point\n examples:\n - value: 22 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000129\n multivalued: false\n alias: dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diether_lipids:\n name: diether_lipids\n annotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of diether lipids; can include multiple types of diether\n lipids\n title: diether lipids\n examples:\n - value: 0.2 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - diether lipids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000178\n multivalued: true\n alias: diether_lipids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n diss_carb_dioxide:\n name: diss_carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved carbon dioxide in the sample or liquid\n portion of the sample\n title: dissolved carbon dioxide\n examples:\n - value: 5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000436\n multivalued: false\n alias: diss_carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_hydrogen:\n name: diss_hydrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved hydrogen\n title: dissolved hydrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved hydrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000179\n multivalued: false\n alias: diss_hydrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_carb:\n name: diss_inorg_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved inorganic carbon concentration in the sample, typically\n measured after filtering the sample using a 0.45 micrometer filter\n title: dissolved inorganic carbon\n examples:\n - value: 2059 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000434\n multivalued: false\n alias: diss_inorg_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_nitro:\n name: diss_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic nitrogen\n title: dissolved inorganic nitrogen\n examples:\n - value: 761 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000698\n multivalued: false\n alias: diss_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_phosp:\n name: diss_inorg_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic phosphorus in the sample\n title: dissolved inorganic phosphorus\n examples:\n - value: 56.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000106\n multivalued: false\n alias: diss_inorg_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_iron:\n name: diss_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved iron in the sample\n title: dissolved iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000139\n multivalued: false\n alias: diss_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_org_carb:\n name: diss_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\n title: dissolved organic carbon\n examples:\n - value: 197 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000433\n multivalued: false\n alias: diss_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_org_nitro:\n name: diss_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\n title: dissolved organic nitrogen\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000162\n multivalued: false\n alias: diss_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_oxygen:\n name: diss_oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen\n title: dissolved oxygen\n examples:\n - value: 175 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000119\n multivalued: false\n alias: diss_oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_oxygen_fluid:\n name: diss_oxygen_fluid\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen in the oil field produced fluids\n as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n title: dissolved oxygen in fluids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen in fluids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000438\n multivalued: false\n alias: diss_oxygen_fluid\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_cont_well:\n name: dna_cont_well\n title: DNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: dna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n door_comp_type:\n name: door_comp_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The composite type of the door\n title: door type, composite\n examples:\n - value: revolving\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, composite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000795\n multivalued: false\n alias: door_comp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_comp_type_enum\n door_cond:\n name: door_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The phsical condition of the door\n title: door condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000788\n multivalued: false\n alias: door_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: door_cond_enum\n door_direct:\n name: door_direct\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction the door opens\n title: door direction of opening\n examples:\n - value: inward\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door direction of opening\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000789\n multivalued: false\n alias: door_direct\n owner: Biosample\n domain_of:\n - Biosample\n range: door_direct_enum\n door_loc:\n name: door_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the door in the room\n title: door location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000790\n multivalued: false\n alias: door_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: door_loc_enum\n door_mat:\n name: door_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the door is composed of\n title: door material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000791\n multivalued: false\n alias: door_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: door_mat_enum\n door_move:\n name: door_move\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of movement of the door\n title: door movement\n examples:\n - value: swinging\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door movement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000792\n multivalued: false\n alias: door_move\n owner: Biosample\n domain_of:\n - Biosample\n range: door_move_enum\n door_size:\n name: door_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the door\n title: door area or size\n examples:\n - value: 2.5 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door area or size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000158\n multivalued: false\n alias: door_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n door_type:\n name: door_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of door material\n title: door type\n examples:\n - value: wooden\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000794\n multivalued: false\n alias: door_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_enum\n door_type_metal:\n name: door_type_metal\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of metal door\n title: door type, metal\n examples:\n - value: hollow\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, metal\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000796\n multivalued: false\n alias: door_type_metal\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_metal_enum\n door_type_wood:\n name: door_type_wood\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of wood door\n title: door type, wood\n examples:\n - value: battened\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, wood\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000797\n multivalued: false\n alias: door_type_wood\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_wood_enum\n door_water_mold:\n name: door_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a door\n title: door signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000793\n multivalued: false\n alias: door_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n down_par:\n name: down_par\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square\n centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Visible waveband radiance and irradiance measurements in the water\n column\n title: downward PAR\n examples:\n - value: 28.71 microEinstein per square meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - downward PAR\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000703\n multivalued: false\n alias: down_par\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n drainage_class:\n name: drainage_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Drainage classification from a standard system such as the USDA system\n title: drainage classification\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drainage classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001085\n multivalued: false\n alias: drainage_class\n owner: Biosample\n domain_of:\n - Biosample\n range: drainage_class_enum\n drawings:\n name: drawings\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The buildings architectural drawings; if design is chosen, indicate\n phase-conceptual, schematic, design development, and construction documents\n title: drawings\n examples:\n - value: sketch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drawings\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000798\n multivalued: false\n alias: drawings\n owner: Biosample\n domain_of:\n - Biosample\n range: drawings_enum\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n efficiency_percent:\n name: efficiency_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of volatile solids removed from the anaerobic digestor\n title: efficiency percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - efficiency percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000657\n multivalued: false\n alias: efficiency_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n elev:\n name: elev\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n multivalued: false\n alias: elev\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n elevator:\n name: elevator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of elevators within the built structure\n title: elevator count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000799\n multivalued: false\n alias: elevator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n emulsions:\n name: emulsions\n annotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as paints, adhesives,\n mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n types\n title: emulsions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - emulsions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000660\n multivalued: true\n alias: emulsions\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n env_broad_scale:\n name: env_broad_scale\n description: 'Report the major environmental system the sample or specimen came\n from. The system(s) identified should have a coarse spatial grain, to provide\n the general environmental context of where the sampling was done (e.g. in the\n desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n title: broad-scale environmental context\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000012\n multivalued: false\n alias: env_broad_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_local_scale:\n name: env_local_scale\n description: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial\n grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n title: local environmental context\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000013\n multivalued: false\n alias: env_local_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_medium:\n name: env_medium\n description: 'Report the environmental material(s) immediately surrounding the\n sample or specimen at the time of sampling. We recommend using subclasses of\n ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference\n mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n (e.g. a tree, a leaf, a table top).'\n title: environmental medium\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000014\n multivalued: false\n alias: env_medium\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_package:\n name: env_package\n description: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the\n name of the environmental package, a selection of fields can be made from the\n subtables and can be reported\n in_subset:\n - mixs extension\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental package\n rank: 1000\n is_a: attribute\n alias: env_package\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n environment field:\n name: environment field\n description: field describing environmental aspect of a sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: environment_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n escalator:\n name: escalator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of escalators within the built structure\n title: escalator count\n examples:\n - value: '4'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - escalator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000800\n multivalued: false\n alias: escalator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ethylbenzene:\n name: ethylbenzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ethylbenzene in the sample\n title: ethylbenzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ethylbenzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000155\n multivalued: false\n alias: ethylbenzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n exp_duct:\n name: exp_duct\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of exposed ductwork in the room\n title: exposed ductwork\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed ductwork\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000144\n multivalued: false\n alias: exp_duct\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n exp_pipe:\n name: exp_pipe\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exposed pipes in the room\n title: exposed pipes\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed pipes\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000220\n multivalued: false\n alias: exp_pipe\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n experimental_factor:\n name: experimental_factor\n annotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\n description: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in\n an increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n title: experimental factor\n examples:\n - value: time series design [EFO:EFO_0001779]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - experimental factor\n rank: 1000\n is_a: investigation field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000008\n multivalued: false\n alias: experimental_factor\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n ext_door:\n name: ext_door\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exterior doors in the built structure\n title: exterior door count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exterior door count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000170\n multivalued: false\n alias: ext_door\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ext_wall_orient:\n name: ext_wall_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The orientation of the exterior wall\n title: orientations of exterior wall\n examples:\n - value: northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior wall\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000817\n multivalued: false\n alias: ext_wall_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_wall_orient_enum\n ext_window_orient:\n name: ext_window_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The compass direction the exterior window of the room is facing\n title: orientations of exterior window\n examples:\n - value: southwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior window\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000818\n multivalued: false\n alias: ext_window_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_window_orient_enum\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n description: Unusual physical events that may have affected microbial populations\n title: history/extreme events\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000320\n multivalued: false\n alias: extreme_event\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n fao_class:\n name: fao_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification from the FAO World Reference Database for Soil\n Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n title: soil_taxonomic/FAO classification\n examples:\n - value: Luvisols\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/FAO classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001083\n multivalued: false\n alias: fao_class\n owner: Biosample\n domain_of:\n - Biosample\n range: fao_class_enum\n fertilizer_regm:\n name: fertilizer_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple fertilizer\n regimens\n title: fertilizer regimen\n examples:\n - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fertilizer regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000556\n multivalued: true\n alias: fertilizer_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n field:\n name: field\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the hydrocarbon field (e.g. Albacora)\n title: field name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - field name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000291\n multivalued: false\n alias: field\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n filter_type:\n name: filter_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: A device which removes solid particulates or airborne molecular contaminants\n title: filter type\n examples:\n - value: HEPA\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - filter type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000765\n multivalued: true\n alias: filter_type\n owner: Biosample\n domain_of:\n - Biosample\n range: filter_type_enum\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of fire\n title: history/fire\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001086\n multivalued: false\n alias: fire\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n fireplace_type:\n name: fireplace_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A firebox with chimney\n title: fireplace type\n examples:\n - value: wood burning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fireplace type\n rank: 1000\n is_a: core field\n string_serialization: '[gas burning|wood burning]'\n slot_uri: MIXS:0000802\n multivalued: false\n alias: fireplace_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of flooding\n title: history/flooding\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000319\n multivalued: false\n alias: flooding\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n floor_age:\n name: floor_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\n description: The time period since installment of the carpet or flooring\n title: floor age\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000164\n multivalued: false\n alias: floor_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_area:\n name: floor_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the floor space within the room\n title: floor area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000165\n multivalued: false\n alias: floor_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_cond:\n name: floor_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the floor at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: floor condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000803\n multivalued: false\n alias: floor_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_cond_enum\n floor_count:\n name: floor_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of floors in the building, including basements and mechanical\n penthouse\n title: floor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000225\n multivalued: false\n alias: floor_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n floor_finish_mat:\n name: floor_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor covering type; the finished surface that is walked on\n title: floor finish material\n examples:\n - value: carpet\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000804\n multivalued: false\n alias: floor_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_finish_mat_enum\n floor_struc:\n name: floor_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\n title: floor structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000806\n multivalued: false\n alias: floor_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_struc_enum\n floor_thermal_mass:\n name: floor_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the floor to provide inertia against temperature fluctuations\n title: floor thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000166\n multivalued: false\n alias: floor_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_water_mold:\n name: floor_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew in a room\n title: floor signs of water/mold\n examples:\n - value: ceiling discoloration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor signs of water/mold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000805\n multivalued: false\n alias: floor_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_water_mold_enum\n fluor:\n name: fluor\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\n description: Raw or converted fluorescence of water\n title: fluorescence\n examples:\n - value: 2.5 volts\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fluorescence\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000704\n multivalued: false\n alias: fluor\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n freq_clean:\n name: freq_clean\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times the sample location is cleaned. Frequency of\n cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n title: frequency of cleaning\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cleaning\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000226\n multivalued: false\n alias: freq_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n freq_cook:\n name: freq_cook\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times a meal is cooked per week\n title: frequency of cooking\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cooking\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000227\n multivalued: false\n alias: freq_cook\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n fungicide_regm:\n name: fungicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fungicide regimens\n title: fungicide regimen\n examples:\n - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fungicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000557\n multivalued: true\n alias: fungicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n furniture:\n name: furniture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The types of furniture present in the sampled room\n title: furniture\n examples:\n - value: chair\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - furniture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000807\n multivalued: false\n alias: furniture\n owner: Biosample\n domain_of:\n - Biosample\n range: furniture_enum\n gaseous_environment:\n name: gaseous_environment\n description: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\n title: gaseous environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000558\n multivalued: true\n alias: gaseous_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gaseous_substances:\n name: gaseous_substances\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\n title: gaseous substances\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous substances\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000661\n multivalued: true\n alias: gaseous_substances\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gender_restroom:\n name: gender_restroom\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The gender type of the restroom\n title: gender of restroom\n examples:\n - value: male\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gender of restroom\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000808\n multivalued: false\n alias: gender_restroom\n owner: Biosample\n domain_of:\n - Biosample\n range: gender_restroom_enum\n genetic_mod:\n name: genetic_mod\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Genetic modifications of the genome of an organism, which may occur\n naturally by spontaneous mutation, or be introduced by some experimental means,\n e.g. specification of a transgene or the gene knocked-out or details of transient\n transfection\n title: genetic modification\n examples:\n - value: aox1A transgenic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - genetic modification\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000859\n multivalued: false\n alias: genetic_mod\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n multivalued: false\n alias: geo_loc_name\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n glucosidase_act:\n name: glucosidase_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of glucosidase activity\n title: glucosidase activity\n examples:\n - value: 5 mol per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - glucosidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000137\n multivalued: false\n alias: glucosidase_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n gravidity:\n name: gravidity\n annotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\n title: gravidity\n examples:\n - value: yes;due date:2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravidity\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{timestamp}'\n slot_uri: MIXS:0000875\n multivalued: false\n alias: gravidity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gravity:\n name: gravity\n annotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity;\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple treatments\n title: gravity\n examples:\n - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000559\n multivalued: true\n alias: gravity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n growth_facil:\n name: growth_facil\n annotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n title: growth facility\n examples:\n - value: Growth chamber [CO_715:0000189]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth facility\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{termLabel} {[termID]}'\n slot_uri: MIXS:0001043\n multivalued: false\n alias: growth_facil\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n growth_habit:\n name: growth_habit\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Characteristic shape, appearance or growth form of a plant species\n title: growth habit\n examples:\n - value: spreading\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth habit\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001044\n multivalued: false\n alias: growth_habit\n owner: Biosample\n domain_of:\n - Biosample\n range: growth_habit_enum\n growth_hormone_regm:\n name: growth_hormone_regm\n annotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple growth\n hormone regimens\n title: growth hormone regimen\n examples:\n - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth hormone regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000560\n multivalued: true\n alias: growth_hormone_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n hall_count:\n name: hall_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of hallways and cooridors in the built structure\n title: hallway/corridor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hallway/corridor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000228\n multivalued: false\n alias: hall_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n handidness:\n name: handidness\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The handidness of the individual sampled\n title: handidness\n examples:\n - value: right handedness\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - handidness\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000809\n multivalued: false\n alias: handidness\n owner: Biosample\n domain_of:\n - Biosample\n range: handidness_enum\n has numeric value:\n name: has numeric value\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_numeric_value\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n has raw value:\n name: has raw value\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n string_serialization: '{has numeric value} {has unit}'\n alias: has_raw_value\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n has unit:\n name: has unit\n description: Example \"m\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_unit\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n hc_produced:\n name: hc_produced\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\n title: hydrocarbon type produced\n examples:\n - value: Gas\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon type produced\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000989\n multivalued: false\n alias: hc_produced\n owner: Biosample\n domain_of:\n - Biosample\n range: hc_produced_enum\n hcr:\n name: hcr\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n defined as a natural environmental feature containing large amounts of hydrocarbons\n at high concentrations potentially suitable for commercial exploitation. This\n term should not be confused with the Hydrocarbon Occurrence term which also\n includes hydrocarbon-rich environments with currently limited commercial interest\n such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n entry in \"additional info\" field\n title: hydrocarbon resource type\n examples:\n - value: Oil Sand\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000988\n multivalued: false\n alias: hcr\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_enum\n hcr_fw_salinity:\n name: hcr_fw_salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original formation water salinity (prior to secondary recovery e.g.\n Waterflooding) expressed as TDS\n title: formation water salinity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - formation water salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000406\n multivalued: false\n alias: hcr_fw_salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n hcr_geol_age:\n name: hcr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: hydrocarbon resource geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000993\n multivalued: false\n alias: hcr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_geol_age_enum\n hcr_pressure:\n name: hcr_pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\n description: Original pressure of the hydrocarbon resource\n title: hydrocarbon resource original pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original pressure\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000395\n multivalued: false\n alias: hcr_pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n hcr_temp:\n name: hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Original temperature of the hydrocarbon resource\n title: hydrocarbon resource original temperature\n examples:\n - value: 150-295 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original temperature\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000393\n multivalued: false\n alias: hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heat_cool_type:\n name: heat_cool_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Methods of conditioning or heating a room or building\n title: heating and cooling system type\n examples:\n - value: heat pump\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating and cooling system type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000766\n multivalued: true\n alias: heat_cool_type\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_cool_type_enum\n heat_deliv_loc:\n name: heat_deliv_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of heat delivery within the room\n title: heating delivery locations\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating delivery locations\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000810\n multivalued: false\n alias: heat_deliv_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_deliv_loc_enum\n heat_sys_deliv_meth:\n name: heat_sys_deliv_meth\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The method by which the heat is delivered through the system\n title: heating system delivery method\n examples:\n - value: radiant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system delivery method\n rank: 1000\n is_a: core field\n string_serialization: '[conductive|radiant]'\n slot_uri: MIXS:0000812\n multivalued: false\n alias: heat_sys_deliv_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n heat_system_id:\n name: heat_system_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The heating system identifier\n title: heating system identifier\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000833\n multivalued: false\n alias: heat_system_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000652\n multivalued: true\n alias: heavy_metals\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heavy_metals_meth:\n name: heavy_metals_meth\n description: Reference or method used in determining heavy metals\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000343\n multivalued: true\n alias: heavy_metals_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n height_carper_fiber:\n name: height_carper_fiber\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average carpet fiber height in the indoor environment\n title: height carpet fiber mat\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - height carpet fiber mat\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000167\n multivalued: false\n alias: height_carper_fiber\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n herbicide_regm:\n name: herbicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of\n herbicide, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple regimens\n title: herbicide regimen\n examples:\n - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - herbicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000561\n multivalued: true\n alias: herbicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n horizon_meth:\n name: horizon_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the horizon\n title: soil horizon method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000321\n multivalued: false\n alias: horizon_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_age:\n name: host_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\n title: host age\n examples:\n - value: 10 days\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000255\n multivalued: false\n alias: host_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_body_habitat:\n name: host_body_habitat\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Original body habitat where the sample was obtained from\n title: host body habitat\n examples:\n - value: nasopharynx\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body habitat\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000866\n multivalued: false\n alias: host_body_habitat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_body_product:\n name: host_body_product\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the body, e.g. Stool, mucus, where the sample\n was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n or https://www.ebi.ac.uk/ols/ontologies/uberon\n title: host body product\n examples:\n - value: Portion of mucus [fma66938]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body product\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000888\n multivalued: false\n alias: host_body_product\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_body_site:\n name: host_body_site\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n title: host body site\n examples:\n - value: gill [UBERON:0002535]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body site\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000867\n multivalued: false\n alias: host_body_site\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_body_temp:\n name: host_body_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Core body temperature of the host when sample was collected\n title: host body temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000274\n multivalued: false\n alias: host_body_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_color:\n name: host_color\n annotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\n description: The color of host\n title: host color\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host color\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000260\n multivalued: false\n alias: host_color\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_common_name:\n name: host_common_name\n annotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\n description: Common name of the host.\n title: host common name\n examples:\n - value: human\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host common name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000248\n multivalued: false\n alias: host_common_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_diet:\n name: host_diet\n annotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\n description: Type of diet depending on the host, for animals omnivore, herbivore\n etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n title: host diet\n examples:\n - value: herbivore\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host diet\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000869\n multivalued: true\n alias: host_diet\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_dry_mass:\n name: host_dry_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of dry mass\n title: host dry mass\n examples:\n - value: 500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host dry mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000257\n multivalued: false\n alias: host_dry_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_family_relation:\n name: host_family_relation\n annotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\n description: Familial relationships to other hosts in the same study; can include\n multiple relationships\n title: host family relationship\n examples:\n - value: offspring;Mussel25\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host family relationship\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0000872\n multivalued: true\n alias: host_family_relation\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_genotype:\n name: host_genotype\n annotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\n description: Observed genotype\n title: host genotype\n examples:\n - value: C57BL/6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host genotype\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000365\n multivalued: false\n alias: host_genotype\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_growth_cond:\n name: host_growth_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Literature reference giving growth conditions of the host\n title: host growth conditions\n examples:\n - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host growth conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000871\n multivalued: false\n alias: host_growth_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_height:\n name: host_height\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The height of subject\n title: host height\n examples:\n - value: 0.1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000264\n multivalued: false\n alias: host_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_last_meal:\n name: host_last_meal\n annotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\n description: Content of last meal and time since feeding; can include multiple\n values\n title: host last meal\n examples:\n - value: corn feed;P2H\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host last meal\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000870\n multivalued: true\n alias: host_last_meal\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_length:\n name: host_length\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length of subject\n title: host length\n examples:\n - value: 1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host length\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000256\n multivalued: false\n alias: host_length\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_life_stage:\n name: host_life_stage\n annotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of life stage of host\n title: host life stage\n examples:\n - value: adult\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host life stage\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000251\n multivalued: false\n alias: host_life_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_phenotype:\n name: host_phenotype\n annotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\n description: Phenotype of human or other host. For phenotypic quality ontology\n (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n title: host phenotype\n examples:\n - value: elongated [PATO:0001154]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host phenotype\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000874\n multivalued: false\n alias: host_phenotype\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_sex:\n name: host_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Gender or physical sex of the host.\n title: host sex\n examples:\n - value: non-binary\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000811\n multivalued: false\n alias: host_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: host_sex_enum\n host_shape:\n name: host_shape\n annotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\n description: Morphological shape of host\n title: host shape\n examples:\n - value: round\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host shape\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000261\n multivalued: false\n alias: host_shape\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_subject_id:\n name: host_subject_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: A unique identifier by which each subject can be referred to, de-identified.\n title: host subject id\n examples:\n - value: MPI123\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subject id\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000861\n multivalued: false\n alias: host_subject_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_subspecf_genlin:\n name: host_subspecf_genlin\n annotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\n description: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n name and the lineage rank separated by a colon, e.g., biovar:abc123.\n title: host subspecific genetic lineage\n examples:\n - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subspecific genetic lineage\n rank: 1000\n is_a: core field\n string_serialization: '{rank name}:{text}'\n slot_uri: MIXS:0001318\n multivalued: true\n alias: host_subspecf_genlin\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_substrate:\n name: host_substrate\n annotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\n description: The growth substrate of the host.\n title: host substrate\n examples:\n - value: rock\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host substrate\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000252\n multivalued: false\n alias: host_substrate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_symbiont:\n name: host_symbiont\n annotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\n description: The taxonomic name of the organism(s) found living in mutualistic,\n commensalistic, or parasitic symbiosis with the specific host.\n title: observed host symbionts\n examples:\n - value: flukeworms\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed host symbionts\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001298\n multivalued: true\n alias: host_symbiont\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_tot_mass:\n name: host_tot_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Total mass of the host at collection, the unit depends on host\n title: host total mass\n examples:\n - value: 2500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host total mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000263\n multivalued: false\n alias: host_tot_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_wet_mass:\n name: host_wet_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of wet mass\n title: host wet mass\n examples:\n - value: 1500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host wet mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000567\n multivalued: false\n alias: host_wet_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n humidity:\n name: humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of water vapour in the air, at the time of sampling\n title: humidity\n examples:\n - value: 25 gram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000100\n multivalued: false\n alias: humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n humidity_regm:\n name: humidity_regm\n annotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying degree\n of humidity; information about treatment involving use of growth hormones; should\n include amount of humidity administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\n title: humidity regimen\n examples:\n - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000568\n multivalued: true\n alias: humidity_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n indoor_space:\n name: indoor_space\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A distinguishable space within a structure, the purpose for which\n discrete areas of a building is used\n title: indoor space\n examples:\n - value: foyer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor space\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000763\n multivalued: false\n alias: indoor_space\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_space_enum\n indoor_surf:\n name: indoor_surf\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of indoor surface\n title: indoor surface\n examples:\n - value: wall\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor surface\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000764\n multivalued: false\n alias: indoor_surf\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_surf_enum\n indust_eff_percent:\n name: indust_eff_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of industrial effluents received by wastewater treatment\n plant\n title: industrial effluent percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - industrial effluent percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000662\n multivalued: false\n alias: indust_eff_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n inorg_particles:\n name: inorg_particles\n annotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\n title: inorganic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inorganic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000664\n multivalued: true\n alias: inorg_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n inside_lux:\n name: inside_lux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded value at sampling time (power density)\n title: inside lux light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inside lux light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000168\n multivalued: false\n alias: inside_lux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n int_wall_cond:\n name: int_wall_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the wall at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: interior wall condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - interior wall condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000813\n multivalued: false\n alias: int_wall_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: int_wall_cond_enum\n investigation field:\n name: investigation field\n description: field describing aspect of the investigation/study to which the sample\n belongs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: investigation_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n iw_bt_date_well:\n name: iw_bt_date_well\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Injection water breakthrough date per well following a secondary\n and/or tertiary recovery\n title: injection water breakthrough date of specific well\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water breakthrough date of specific well\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001010\n multivalued: false\n alias: iw_bt_date_well\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n iwf:\n name: iwf\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Proportion of the produced fluids derived from injected water at\n the time of sampling. (e.g. 87%)\n title: injection water fraction\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water fraction\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000455\n multivalued: false\n alias: iwf\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n last_clean:\n name: last_clean\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The last time the floor was cleaned (swept, mopped, vacuumed)\n title: last time swept/mopped/vacuumed\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - last time swept/mopped/vacuumed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000814\n multivalued: false\n alias: last_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n lat_lon:\n name: lat_lon\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n multivalued: false\n alias: lat_lon\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n lbc_thirty:\n name: lbc_thirty\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined after 30 minute incubation\n title: lime buffer capacity (at 30 minutes)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 543 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n aliases:\n - lbc_thirty\n - lbc30\n - lime buffer capacity (at 30 minutes)\n rank: 1000\n is_a: attribute\n alias: lbc_thirty\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n lbceq:\n name: lbceq\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined at equilibrium after 5 day incubation\n title: lime buffer capacity (after 5 day incubation)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 1575 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - lbceq\n - lime buffer capacity (at 5-day equilibrium)\n rank: 1000\n is_a: attribute\n alias: lbceq\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_intensity:\n name: light_intensity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of light intensity\n title: light intensity\n examples:\n - value: 0.3 lux\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light intensity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000706\n multivalued: false\n alias: light_intensity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_regm:\n name: light_regm\n annotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\n title: light regimen\n examples:\n - value: incandescant light;10 lux;450 nanometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000569\n multivalued: false\n alias: light_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n light_type:\n name: light_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Application of light to achieve some practical or aesthetic effect.\n Lighting includes the use of both artificial light sources such as lamps and\n light fixtures, as well as natural illumination by capturing daylight. Can also\n include absence of light\n title: light type\n examples:\n - value: desk lamp\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000769\n multivalued: true\n alias: light_type\n owner: Biosample\n domain_of:\n - Biosample\n range: light_type_enum\n link_addit_analys:\n name: link_addit_analys\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to additional analysis results performed on the sample\n title: links to additional analysis\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - links to additional analysis\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000340\n multivalued: false\n alias: link_addit_analys\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n link_class_info:\n name: link_class_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to digitized soil maps or other soil classification information\n title: link to classification information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to classification information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000329\n multivalued: false\n alias: link_class_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n link_climate_info:\n name: link_climate_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to climate resource\n title: link to climate information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to climate information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000328\n multivalued: false\n alias: link_climate_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n lithology:\n name: lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: lithology\n examples:\n - value: Volcanic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000990\n multivalued: false\n alias: lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: lithology_enum\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n multivalued: false\n alias: local_class\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n local_class_meth:\n name: local_class_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the local soil classification\n title: soil_taxonomic/local classification method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000331\n multivalued: false\n alias: local_class_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n magnesium:\n name: magnesium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per\n kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of magnesium in the sample\n title: magnesium\n examples:\n - value: 52.8 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - magnesium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000431\n multivalued: false\n alias: magnesium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n manganese:\n name: manganese\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of manganese in the sample\n title: manganese\n examples:\n - value: 24.7 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - manganese\n rank: 1000\n is_a: attribute\n alias: manganese\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n max_occup:\n name: max_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The maximum amount of people allowed in the indoor environment\n title: maximum occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - maximum occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000229\n multivalued: false\n alias: max_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mean_frict_vel:\n name: mean_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean friction velocity\n title: mean friction velocity\n examples:\n - value: 0.5 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000498\n multivalued: false\n alias: mean_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mean_peak_frict_vel:\n name: mean_peak_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean peak friction velocity\n title: mean peak friction velocity\n examples:\n - value: 1 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean peak friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000502\n multivalued: false\n alias: mean_peak_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mech_struc:\n name: mech_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'mechanical structure: a moving structure'\n title: mechanical structure\n examples:\n - value: elevator\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000815\n multivalued: false\n alias: mech_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: mech_struc_enum\n mechanical_damage:\n name: mechanical_damage\n annotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\n description: Information about any mechanical damage exerted on the plant; can\n include multiple damages and sites\n title: mechanical damage\n examples:\n - value: pruning;bark\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical damage\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0001052\n multivalued: true\n alias: mechanical_damage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n methane:\n name: methane\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Methane (gas) amount or concentration at the time of sampling\n title: methane\n examples:\n - value: 1800 parts per billion\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - methane\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000101\n multivalued: false\n alias: methane\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n micro_biomass_meth:\n name: micro_biomass_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining microbial biomass\n title: microbial biomass method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000339\n multivalued: false\n alias: micro_biomass_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n microbial_biomass:\n name: microbial_biomass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n to have correction factors used for conversion to the final units\n title: microbial biomass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000650\n multivalued: false\n alias: microbial_biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mineral_nutr_regm:\n name: mineral_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n mineral nutrient regimens\n title: mineral nutrient regimen\n examples:\n - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000570\n multivalued: true\n alias: mineral_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n misc_param:\n name: misc_param\n annotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Any other measurement performed or parameter collected, that is not\n listed here\n title: miscellaneous parameter\n examples:\n - value: Bicarbonate ion concentration;2075 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - miscellaneous parameter\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000752\n multivalued: true\n alias: misc_param\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n n_alkanes:\n name: n_alkanes\n annotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of n-alkanes; can include multiple n-alkanes\n title: n-alkanes\n examples:\n - value: n-hexadecane;100 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - n-alkanes\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000503\n multivalued: true\n alias: n_alkanes\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n nitrate:\n name: nitrate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate in the sample\n title: nitrate\n examples:\n - value: 65 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000425\n multivalued: false\n alias: nitrate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrate_nitrogen:\n name: nitrate_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate nitrogen in the sample\n title: nitrate_nitrogen\n comments:\n - often below some specified limit of detection\n examples:\n - value: 0.29 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrate_nitrogen\n - NO3-N\n rank: 1000\n is_a: attribute\n alias: nitrate_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite:\n name: nitrite\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite in the sample\n title: nitrite\n examples:\n - value: 0.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000426\n multivalued: false\n alias: nitrite\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite_nitrogen:\n name: nitrite_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite nitrogen in the sample\n title: nitrite_nitrogen\n examples:\n - value: 1.2 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrite_nitrogen\n - NO2-N\n rank: 1000\n is_a: attribute\n alias: nitrite_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitro:\n name: nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrogen (total)\n title: nitrogen\n examples:\n - value: 4.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000504\n multivalued: false\n alias: nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n non_min_nutr_regm:\n name: non_min_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple non-mineral nutrient regimens\n title: non-mineral nutrient regimen\n examples:\n - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - non-mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000571\n multivalued: true\n alias: non_min_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n multivalued: false\n alias: nucl_acid_amp\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucl_acid_ext:\n name: nucl_acid_ext\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the material separation to recover\n the nucleic acid fraction from a sample\n title: nucleic acid extraction\n examples:\n - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid extraction\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000037\n multivalued: false\n alias: nucl_acid_ext\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucleic acid sequence source field:\n name: nucleic acid sequence source field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: nucleic_acid_sequence_source_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n number_pets:\n name: number_pets\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of pets residing in the sampled space\n title: number of pets\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of pets\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000231\n multivalued: false\n alias: number_pets\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n number_plants:\n name: number_plants\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of plant(s) in the sampling space\n title: number of houseplants\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of houseplants\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000230\n multivalued: false\n alias: number_plants\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n number_resident:\n name: number_resident\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of individuals currently occupying in the sampling location\n title: number of residents\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of residents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000232\n multivalued: false\n alias: number_resident\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n occup_density_samp:\n name: occup_density_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Average number of occupants at time of sampling per square footage\n title: occupant density at sampling\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupant density at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000217\n multivalued: false\n alias: occup_density_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n occup_document:\n name: occup_document\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of documentation of occupancy\n title: occupancy documentation\n examples:\n - value: estimate\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy documentation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000816\n multivalued: false\n alias: occup_document\n owner: Biosample\n domain_of:\n - Biosample\n range: occup_document_enum\n occup_samp:\n name: occup_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of occupants present at time of sample within the given space\n title: occupancy at sampling\n examples:\n - value: '10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000772\n multivalued: false\n alias: occup_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_carb:\n name: org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic carbon\n title: organic carbon\n examples:\n - value: 1.5 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000508\n multivalued: false\n alias: org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_count_qpcr_info:\n name: org_count_qpcr_info\n annotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\n description: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\n title: organism count qPCR information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count qPCR information\n rank: 1000\n is_a: core field\n string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\n slot_uri: MIXS:0000099\n multivalued: false\n alias: org_count_qpcr_info\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n org_matter:\n name: org_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic matter\n title: organic matter\n examples:\n - value: 1.75 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000204\n multivalued: false\n alias: org_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_nitro:\n name: org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic nitrogen\n title: organic nitrogen\n examples:\n - value: 4 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000205\n multivalued: false\n alias: org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_particles:\n name: org_particles\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\n title: organic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000665\n multivalued: true\n alias: org_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n organism_count:\n name: organism_count\n annotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\n description: 'Total cell count of any organism (or group of organisms) per gram,\n volume or area of sample, should include name of organism followed by count.\n The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n title: organism count\n examples:\n - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000103\n multivalued: true\n alias: organism_count\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n owc_tvdss:\n name: owc_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n title: oil water contact depth\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oil water contact depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000405\n multivalued: false\n alias: owc_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n oxy_stat_samp:\n name: oxy_stat_samp\n description: Oxygenation status of sample\n title: oxygenation status of sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000753\n multivalued: false\n alias: oxy_stat_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n oxygen:\n name: oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygen (gas) amount or concentration at the time of sampling\n title: oxygen\n examples:\n - value: 600 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000104\n multivalued: false\n alias: oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n part_org_carb:\n name: part_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic carbon\n title: particulate organic carbon\n examples:\n - value: 1.92 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000515\n multivalued: false\n alias: part_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n part_org_nitro:\n name: part_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic nitrogen\n title: particulate organic nitrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000719\n multivalued: false\n alias: part_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n particle_class:\n name: particle_class\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\n description: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle\n preceded by the name of the particle type; can include multiple values\n title: particle classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particle classification\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000206\n multivalued: true\n alias: particle_class\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n multivalued: false\n alias: pcr_cond\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n multivalued: false\n alias: pcr_primers\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n permeability:\n name: permeability\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n title: permeability\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - permeability\n rank: 1000\n is_a: core field\n string_serialization: '{integer} - {integer} {unit}'\n slot_uri: MIXS:0000404\n multivalued: false\n alias: permeability\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n perturbation:\n name: perturbation\n annotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time\n of the entire perturbation period; can include multiple perturbation types\n title: perturbation\n examples:\n - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - perturbation\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000754\n multivalued: true\n alias: perturbation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pesticide_regm:\n name: pesticide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of insecticides; should\n include the name of pesticide, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple pesticide\n regimens\n title: pesticide regimen\n examples:\n - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pesticide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000573\n multivalued: true\n alias: pesticide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n petroleum_hydrocarb:\n name: petroleum_hydrocarb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of petroleum hydrocarbon\n title: petroleum hydrocarbon\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - petroleum hydrocarbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000516\n multivalued: false\n alias: petroleum_hydrocarb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ph:\n name: ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\n title: pH\n examples:\n - value: '7.2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001001\n multivalued: false\n alias: ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n ph_meth:\n name: ph_meth\n description: Reference or method used in determining ph\n title: pH method\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001106\n multivalued: false\n alias: ph_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ph_regm:\n name: ph_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plants to varying\n levels of ph of the growth media, treatment regimen including how many times\n the treatment was repeated, how long each treatment lasted, and the start and\n end time of the entire treatment; can include multiple regimen\n title: pH regimen\n examples:\n - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001056\n multivalued: true\n alias: ph_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n phaeopigments:\n name: phaeopigments\n annotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phaeopigments; can include multiple phaeopigments\n title: phaeopigments\n examples:\n - value: 2.5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phaeopigments\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000180\n multivalued: true\n alias: phaeopigments\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n phosphate:\n name: phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of phosphate\n title: phosphate\n examples:\n - value: 0.7 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000505\n multivalued: false\n alias: phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n phosplipid_fatt_acid:\n name: phosplipid_fatt_acid\n annotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phospholipid fatty acids; can include multiple values\n title: phospholipid fatty acid\n examples:\n - value: 2.98 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phospholipid fatty acid\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000181\n multivalued: true\n alias: phosplipid_fatt_acid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n photon_flux:\n name: photon_flux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of photon flux\n title: photon flux\n examples:\n - value: 3.926 micromole photons per second per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - photon flux\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000725\n multivalued: false\n alias: photon_flux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n plant_growth_med:\n name: plant_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n vitro liquid culture medium. Recommended value is a specific value from EO:plant\n growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n or other controlled vocabulary\n title: plant growth medium\n examples:\n - value: hydroponic plant culture media [EO:0007067]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant growth medium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001057\n multivalued: false\n alias: plant_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n plant_product:\n name: plant_product\n annotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the plant, where the sample was obtained from\n title: plant product\n examples:\n - value: xylem sap [PO:0025539]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant product\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001058\n multivalued: false\n alias: plant_product\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n plant_sex:\n name: plant_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n staminate, monoecieous, hermaphrodite.\n title: plant sex\n examples:\n - value: Hermaphroditic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001059\n multivalued: false\n alias: plant_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: plant_sex_enum\n plant_struc:\n name: plant_struc\n annotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n sex of it can be recorded here.\n title: plant structure\n examples:\n - value: epidermis [PO:0005679]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant structure\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0001060\n multivalued: false\n alias: plant_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n pollutants:\n name: pollutants\n annotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Pollutant types and, amount or concentrations measured at the time\n of sampling; can report multiple pollutants by entering numeric values preceded\n by name of pollutant\n title: pollutants\n examples:\n - value: lead;0.15 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pollutants\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000107\n multivalued: true\n alias: pollutants\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pool_dna_extracts:\n name: pool_dna_extracts\n annotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\n description: Indicate whether multiple DNA extractions were mixed. If the answer\n yes, the number of extracts that were pooled should be given\n title: pooling of DNA extracts (if done)\n examples:\n - value: yes;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pooling of DNA extracts (if done)\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{integer}'\n slot_uri: MIXS:0000325\n multivalued: false\n alias: pool_dna_extracts\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n porosity:\n name: porosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Porosity of deposited sediment is volume of voids divided by the\n total volume of sample\n title: porosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - porosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000211\n multivalued: false\n alias: porosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n potassium:\n name: potassium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of potassium in the sample\n title: potassium\n examples:\n - value: 463 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - potassium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000430\n multivalued: false\n alias: potassium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n pour_point:\n name: pour_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n a high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n title: pour point\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pour point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000127\n multivalued: false\n alias: pour_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n pre_treatment:\n name: pre_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process of pre-treatment removes materials that can be easily\n collected from the raw wastewater\n title: pre-treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pre-treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000348\n multivalued: false\n alias: pre_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pres_animal_insect:\n name: pres_animal_insect\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\n description: The type and number of animals or insects present in the sampling\n space.\n title: presence of pets, animals, or insects\n examples:\n - value: cat;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - presence of pets, animals, or insects\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000819\n multivalued: false\n alias: pres_animal_insect\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n pattern: ^(cat|dog|rodent|snake|other);\\d+$\n pressure:\n name: pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\n description: Pressure to which the sample is subject to, in atmospheres\n title: pressure\n examples:\n - value: 50 atmosphere\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000412\n multivalued: false\n alias: pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n prev_land_use_meth:\n name: prev_land_use_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining previous land use and dates\n title: history/previous land use method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000316\n multivalued: false\n alias: prev_land_use_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n previous_land_use:\n name: previous_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\n description: Previous land use and dates\n title: history/previous land use\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use\n rank: 1000\n is_a: core field\n string_serialization: '{text};{timestamp}'\n slot_uri: MIXS:0000315\n multivalued: false\n alias: previous_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n primary_prod:\n name: primary_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of primary production, generally measured as isotope\n uptake\n title: primary production\n examples:\n - value: 100 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000728\n multivalued: false\n alias: primary_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n primary_treatment:\n name: primary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process to produce both a generally homogeneous liquid capable\n of being treated biologically and a sludge that can be separately treated or\n processed\n title: primary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000349\n multivalued: false\n alias: primary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n prod_rate:\n name: prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n title: production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000452\n multivalued: false\n alias: prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n prod_start_date:\n name: prod_start_date\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Date of field's first production\n title: production start date\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001008\n multivalued: false\n alias: prod_start_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n profile_position:\n name: profile_position\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\n title: profile position\n examples:\n - value: summit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - profile position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001084\n multivalued: false\n alias: profile_position\n owner: Biosample\n domain_of:\n - Biosample\n range: profile_position_enum\n quad_pos:\n name: quad_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The quadrant position of the sampling room within the building\n title: quadrant position\n examples:\n - value: West side\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - quadrant position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000820\n multivalued: false\n alias: quad_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: quad_pos_enum\n radiation_regm:\n name: radiation_regm\n annotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plant or a plant\n part to a particular radiation regimen; should include the radiation type, amount\n or intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple radiation regimens\n title: radiation regimen\n examples:\n - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - radiation regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000575\n multivalued: true\n alias: radiation_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n rainfall_regm:\n name: rainfall_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to a given amount\n of rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\n title: rainfall regimen\n examples:\n - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rainfall regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000576\n multivalued: true\n alias: rainfall_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n reactor_type:\n name: reactor_type\n annotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Anaerobic digesters can be designed and engineered to operate using\n a number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\n title: reactor type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reactor type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000350\n multivalued: false\n alias: reactor_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n redox_potential:\n name: redox_potential\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\n description: Redox potential, measured relative to a hydrogen cell, indicating\n oxidation or reduction potential\n title: redox potential\n examples:\n - value: 300 millivolt\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - redox potential\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000182\n multivalued: false\n alias: redox_potential\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_air_humidity:\n name: rel_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Partial vapor and air pressure, density of the vapor and air, or\n by the actual mass of the vapor and air\n title: relative air humidity\n examples:\n - value: 80%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000121\n multivalued: false\n alias: rel_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_humidity_out:\n name: rel_humidity_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded outside relative humidity value at the time of sampling\n title: outside relative humidity\n examples:\n - value: 12 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - outside relative humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000188\n multivalued: false\n alias: rel_humidity_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_samp_loc:\n name: rel_samp_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The sampling location within the train car\n title: relative sampling location\n examples:\n - value: center of car\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative sampling location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000821\n multivalued: false\n alias: rel_samp_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: rel_samp_loc_enum\n reservoir:\n name: reservoir\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the reservoir (e.g. Carapebus)\n title: reservoir name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reservoir name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000303\n multivalued: false\n alias: reservoir\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n resins_pc:\n name: resins_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: resins wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - resins wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000134\n multivalued: false\n alias: resins_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_air_exch_rate:\n name: room_air_exch_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The rate at which outside air replaces indoor air in a given space\n title: room air exchange rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room air exchange rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000169\n multivalued: false\n alias: room_air_exch_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n room_architec_elem:\n name: room_architec_elem\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\n title: room architectural elements\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room architectural elements\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000233\n multivalued: false\n alias: room_architec_elem\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n room_condt:\n name: room_condt\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The condition of the room at the time of sampling\n title: room condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000822\n multivalued: false\n alias: room_condt\n owner: Biosample\n domain_of:\n - Biosample\n range: room_condt_enum\n room_connected:\n name: room_connected\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms connected to the sampling room by a doorway\n title: rooms connected by a doorway\n examples:\n - value: office\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms connected by a doorway\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000826\n multivalued: false\n alias: room_connected\n owner: Biosample\n domain_of:\n - Biosample\n range: room_connected_enum\n room_count:\n name: room_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of rooms in the built structure including all room\n types\n title: room count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000234\n multivalued: false\n alias: room_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_dim:\n name: room_dim\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length, width and height of sampling room\n title: room dimensions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room dimensions\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n slot_uri: MIXS:0000192\n multivalued: false\n alias: room_dim\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_door_dist:\n name: room_door_dist\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Distance between doors (meters) in the hallway between the sampling\n room and adjacent rooms\n title: room door distance\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room door distance\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000193\n multivalued: false\n alias: room_door_dist\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_door_share:\n name: room_door_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a door with the\n sampling room\n title: rooms that share a door with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a door with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000242\n multivalued: false\n alias: room_door_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_hallway:\n name: room_hallway\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) located in the same hallway\n as sampling room\n title: rooms that are on the same hallway\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that are on the same hallway\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000238\n multivalued: false\n alias: room_hallway\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_loc:\n name: room_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The position of the room within the building\n title: room location in building\n examples:\n - value: interior room\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room location in building\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000823\n multivalued: false\n alias: room_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: room_loc_enum\n room_moist_dam_hist:\n name: room_moist_dam_hist\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\n title: room moisture damage or mold history\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room moisture damage or mold history\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000235\n multivalued: false\n alias: room_moist_dam_hist\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n room_net_area:\n name: room_net_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The net floor area of sampling room. Net area excludes wall thicknesses\n title: room net area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room net area\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000194\n multivalued: false\n alias: room_net_area\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_occup:\n name: room_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Count of room occupancy at time of sampling\n title: room occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000236\n multivalued: false\n alias: room_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n room_samp_pos:\n name: room_samp_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal sampling position in the room relative to architectural\n elements\n title: room sampling position\n examples:\n - value: south corner\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room sampling position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000824\n multivalued: false\n alias: room_samp_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: room_samp_pos_enum\n room_type:\n name: room_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The main purpose or activity of the sampling room. A room is any\n distinguishable space within a structure\n title: room type\n examples:\n - value: bathroom\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000825\n multivalued: false\n alias: room_type\n owner: Biosample\n domain_of:\n - Biosample\n range: room_type_enum\n room_vol:\n name: room_vol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Volume of sampling room\n title: room volume\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room volume\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000195\n multivalued: false\n alias: room_vol\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_wall_share:\n name: room_wall_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a wall with the\n sampling room\n title: rooms that share a wall with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a wall with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000243\n multivalued: false\n alias: room_wall_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_window_count:\n name: room_window_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of windows in the room\n title: room window count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room window count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000237\n multivalued: false\n alias: room_window_count\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n root_cond:\n name: root_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\n title: rooting conditions\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001061\n multivalued: false\n alias: root_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_carbon:\n name: root_med_carbon\n annotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n title: rooting medium carbon\n examples:\n - value: sucrose\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium carbon\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000577\n multivalued: false\n alias: root_med_carbon\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_macronutr:\n name: root_med_macronutr\n annotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium macronutrients (N,P, K,\n Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n title: rooting medium macronutrients\n examples:\n - value: KH2PO4;170\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium macronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000578\n multivalued: false\n alias: root_med_macronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_micronutr:\n name: root_med_micronutr\n annotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n title: rooting medium micronutrients\n examples:\n - value: H3BO3;6.2\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium micronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000579\n multivalued: false\n alias: root_med_micronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_ph:\n name: root_med_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: pH measurement of the culture rooting medium; e.g. 5.5.\n title: rooting medium pH\n examples:\n - value: '7.5'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001062\n multivalued: false\n alias: root_med_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n root_med_regl:\n name: root_med_regl\n annotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Growth regulators in the culture rooting medium such as cytokinins,\n auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n title: rooting medium regulators\n examples:\n - value: abscisic acid;0.75 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium regulators\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000581\n multivalued: false\n alias: root_med_regl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_solid:\n name: root_med_solid\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\n title: rooting medium solidifier\n examples:\n - value: agar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium solidifier\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001063\n multivalued: false\n alias: root_med_solid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_suppl:\n name: root_med_suppl\n annotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\n title: rooting medium organic supplements\n examples:\n - value: nicotinic acid;0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium organic supplements\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000580\n multivalued: false\n alias: root_med_suppl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n salinity:\n name: salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The total concentration of all dissolved salts in a liquid or solid\n sample. While salinity can be measured by a complete chemical analysis, this\n method is difficult and time consuming. More often, it is instead derived from\n the conductivity measurement. This is known as practical salinity. These derivations\n compare the specific conductance of the sample to a salinity standard such as\n seawater.\n title: salinity\n examples:\n - value: 25 practical salinity unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000183\n multivalued: false\n alias: salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n salinity_meth:\n name: salinity_meth\n description: Reference or method used in determining salinity\n title: salinity method\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000341\n multivalued: false\n alias: salinity_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n salt_regm:\n name: salt_regm\n annotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of salts as supplement\n to liquid and soil growth media; should include the name of salt, amount administered,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple salt regimens\n title: salt regimen\n examples:\n - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salt regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000582\n multivalued: true\n alias: salt_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_capt_status:\n name: samp_capt_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Reason for the sample\n title: sample capture status\n examples:\n - value: farm sample\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample capture status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000860\n multivalued: false\n alias: samp_capt_status\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_capt_status_enum\n samp_collec_device:\n name: samp_collec_device\n annotations:\n expected_value:\n tag: expected_value\n value: device name\n description: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n title: sample collection device\n examples:\n - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection device\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000002\n multivalued: false\n alias: samp_collec_device\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n samp_collec_method:\n name: samp_collec_method\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\n description: The method employed for collecting the sample.\n title: sample collection method\n examples:\n - value: swabbing\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection method\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001225\n multivalued: false\n alias: samp_collec_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n samp_collect_point:\n name: samp_collect_point\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry\n in \"additional info\" field\n title: sample collection point\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001015\n multivalued: false\n alias: samp_collect_point\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_collect_point_enum\n samp_dis_stage:\n name: samp_dis_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\n title: sample disease stage\n examples:\n - value: infection\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample disease stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000249\n multivalued: false\n alias: samp_dis_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_dis_stage_enum\n samp_floor:\n name: samp_floor\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor of the building, where the sampling room is located\n title: sampling floor\n examples:\n - value: 4th floor\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling floor\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000828\n multivalued: false\n alias: samp_floor\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_floor_enum\n samp_loc_corr_rate:\n name: samp_loc_corr_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\n description: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short\n term rates and for that reason they are preferred during reporting. In the case\n of suspected MIC, corrosion rate measurements at the time of sampling might\n provide insights into the involvement of certain microbial community members\n in MIC as well as potential microbial interplays\n title: corrosion rate at sample location\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - corrosion rate at sample location\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000136\n multivalued: false\n alias: samp_loc_corr_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_mat_process:\n name: samp_mat_process\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A brief description of any processing applied to the sample during\n or after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\n title: sample material processing\n examples:\n - value: filtering of seawater, storing samples in ethanol\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample material processing\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000016\n multivalued: false\n alias: samp_mat_process\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n samp_md:\n name: samp_md\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: In non deviated well, measured depth is equal to the true vertical\n depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n wells, the MD is the length of trajectory of the borehole measured from the\n same reference or datum. Common datums used are ground level (GL), drilling\n rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: sample measured depth\n examples:\n - value: 1534 meter;MSL\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample measured depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000413\n multivalued: false\n alias: samp_md\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_preserv:\n name: samp_preserv\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\n description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n title: preservative added to sample\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - preservative added to sample\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000463\n multivalued: false\n alias: samp_preserv\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_room_id:\n name: samp_room_id\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\n title: sampling room ID or name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling room ID or name\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000244\n multivalued: false\n alias: samp_room_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_size:\n name: samp_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample collected.\n title: amount or size of sample collected\n examples:\n - value: 5 liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount or size of sample collected\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000001\n multivalued: false\n alias: samp_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_sort_meth:\n name: samp_sort_meth\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\n description: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers\n in diameter, where common values of X would be 10 and 2.5 full size sorting\n in a cascade impactor.\n title: sample size sorting method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample size sorting method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000216\n multivalued: true\n alias: samp_sort_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_dur:\n name: samp_store_dur\n annotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Duration for which the sample was stored\n title: sample storage duration\n examples:\n - value: P1Y6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage duration\n rank: 1000\n is_a: core field\n string_serialization: '{duration}'\n slot_uri: MIXS:0000116\n multivalued: false\n alias: samp_store_dur\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_loc:\n name: samp_store_loc\n annotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\n description: Location at which sample was stored, usually name of a specific freezer/room\n title: sample storage location\n examples:\n - value: Freezer no:5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage location\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000755\n multivalued: false\n alias: samp_store_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_temp:\n name: samp_store_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature at which sample was stored, e.g. -80 degree Celsius\n title: sample storage temperature\n examples:\n - value: -80 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000110\n multivalued: false\n alias: samp_store_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_subtype:\n name: samp_subtype\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n please propose entry in \"additional info\" field\n title: sample subtype\n examples:\n - value: biofilm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample subtype\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000999\n multivalued: false\n alias: samp_subtype\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_subtype_enum\n samp_taxon_id:\n name: samp_taxon_id\n annotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\n description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\n sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n 'blank sample' for negative controls.\n title: Taxonomy ID of DNA sample\n comments:\n - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Taxonomy ID of DNA sample\n rank: 1000\n is_a: investigation field\n slot_uri: MIXS:0001320\n multivalued: false\n alias: samp_taxon_id\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n samp_time_out:\n name: samp_time_out\n annotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The recent and long term history of outside sampling\n title: sampling time outside\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling time outside\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000196\n multivalued: false\n alias: samp_time_out\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_transport_cond:\n name: samp_transport_cond\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n title: sample transport conditions\n examples:\n - value: 5 days;-20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample transport conditions\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000410\n multivalued: false\n alias: samp_transport_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_tvdss:\n name: samp_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\n title: sample true vertical depth subsea\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample true vertical depth subsea\n rank: 1000\n is_a: core field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000409\n multivalued: false\n alias: samp_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_type:\n name: samp_type\n annotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material from which the sample was obtained. For the\n Hydrocarbon package, samples include types like core, rock trimmings, drill\n cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n produced water, injected water, swabs, etc. For the Food Package, samples are\n usually categorized as food, body products or tissues, or environmental material.\n This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n title: sample type\n examples:\n - value: built environment sample [GENEPIO:0001248]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000998\n multivalued: false\n alias: samp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_vol_we_dna_ext:\n name: samp_vol_we_dna_ext\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\n description: 'Volume (ml) or mass (g) of total collected sample processed for\n DNA extraction. Note: total sample collected should be entered under the term\n Sample Size (MIXS:0000001).'\n title: sample volume or weight for DNA extraction\n examples:\n - value: 1500 milliliter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample volume or weight for DNA extraction\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000111\n multivalued: false\n alias: samp_vol_we_dna_ext\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: QuantityValue\n samp_weather:\n name: samp_weather\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The weather on the sampling day\n title: sampling day weather\n examples:\n - value: foggy\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling day weather\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000827\n multivalued: false\n alias: samp_weather\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_weather_enum\n samp_well_name:\n name: samp_well_name\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the well (e.g. BXA1123) where sample was taken\n title: sample well name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample well name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000296\n multivalued: false\n alias: samp_well_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n saturates_pc:\n name: saturates_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: saturates wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - saturates wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000131\n multivalued: false\n alias: saturates_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season:\n name: season\n annotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\n description: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms\n listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n title: season\n examples:\n - value: autumn [NCIT:C94733]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - season\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000829\n multivalued: false\n alias: season\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season_environment:\n name: season_environment\n annotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment\n title: seasonal environment\n examples:\n - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001068\n multivalued: true\n alias: season_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season_precpt:\n name: season_precpt\n description: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000645\n multivalued: false\n alias: season_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n season_temp:\n name: season_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean seasonal temperature\n title: mean seasonal temperature\n examples:\n - value: 18 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000643\n multivalued: false\n alias: season_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n season_use:\n name: season_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The seasons the space is occupied\n title: seasonal use\n examples:\n - value: Winter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000830\n multivalued: false\n alias: season_use\n owner: Biosample\n domain_of:\n - Biosample\n range: season_use_enum\n secondary_treatment:\n name: secondary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process for substantially degrading the biological content of\n the sewage\n title: secondary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000351\n multivalued: false\n alias: secondary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n sediment_type:\n name: sediment_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about the sediment type based on major constituents\n title: sediment type\n examples:\n - value: biogenous\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sediment type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001078\n multivalued: false\n alias: sediment_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sediment_type_enum\n seq_meth:\n name: seq_meth\n annotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\n description: Sequencing machine used. Where possible the term should be taken\n from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\n title: sequencing method\n examples:\n - value: 454 Genome Sequencer FLX [OBI:0000702]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequencing method\n rank: 1000\n is_a: sequencing field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000050\n multivalued: false\n alias: seq_meth\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n seq_quality_check:\n name: seq_quality_check\n annotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\n description: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or\n chromatograms). Applied only for sequences that are not submitted to SRA,ENA\n or DRA\n title: sequence quality check\n examples:\n - value: none\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequence quality check\n rank: 1000\n is_a: sequencing field\n string_serialization: '[none|manually edited]'\n slot_uri: MIXS:0000051\n multivalued: false\n alias: seq_quality_check\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n sequencing field:\n name: sequencing field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: sequencing_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sewage_type:\n name: sewage_type\n annotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of wastewater treatment plant as municipial or industrial\n title: sewage type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sewage type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000215\n multivalued: false\n alias: sewage_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shad_dev_water_mold:\n name: shad_dev_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the shading device\n title: shading device signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000834\n multivalued: false\n alias: shad_dev_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n shading_device_cond:\n name: shading_device_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the shading device at the time of sampling\n title: shading device condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000831\n multivalued: false\n alias: shading_device_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_cond_enum\n shading_device_loc:\n name: shading_device_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of the shading device in relation to the built structure\n title: shading device location\n examples:\n - value: exterior\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device location\n rank: 1000\n is_a: core field\n string_serialization: '[exterior|interior]'\n slot_uri: MIXS:0000832\n multivalued: false\n alias: shading_device_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shading_device_mat:\n name: shading_device_mat\n annotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the shading device is composed of\n title: shading device material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device material\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000245\n multivalued: false\n alias: shading_device_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shading_device_type:\n name: shading_device_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of shading device\n title: shading device type\n examples:\n - value: slatted aluminum awning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000835\n multivalued: false\n alias: shading_device_type\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_type_enum\n sieving:\n name: sieving\n description: Collection design of pooled samples and/or sieve size and amount\n of sample sieved\n title: composite design/sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n slot_uri: MIXS:0000322\n multivalued: false\n alias: sieving\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n silicate:\n name: silicate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of silicate\n title: silicate\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - silicate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000184\n multivalued: false\n alias: silicate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n size_frac:\n name: size_frac\n annotations:\n expected_value:\n tag: expected_value\n value: filter size value range\n description: Filtering pore size used in sample preparation\n title: size fraction selected\n examples:\n - value: 0-0.22 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size fraction selected\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000017\n multivalued: false\n alias: size_frac\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n size_frac_low:\n name: size_frac_low\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\n title: size-fraction lower threshold\n examples:\n - value: 0.2 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction lower threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000735\n multivalued: false\n alias: size_frac_low\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n size_frac_up:\n name: size_frac_up\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to retain the sample. Materials\n smaller than the size threshold are excluded from the sample\n title: size-fraction upper threshold\n examples:\n - value: 20 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction upper threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000736\n multivalued: false\n alias: size_frac_up\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n title: slope aspect\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000647\n multivalued: false\n alias: slope_aspect\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n slope_gradient:\n name: slope_gradient\n description: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This\n measure is usually taken with a hand level meter or clinometer\n title: slope gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000646\n multivalued: false\n alias: slope_gradient\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sludge_retent_time:\n name: sludge_retent_time\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\n description: The time activated sludge remains in reactor\n title: sludge retention time\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sludge retention time\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000669\n multivalued: false\n alias: sludge_retent_time\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sodium:\n name: sodium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Sodium concentration in the sample\n title: sodium\n examples:\n - value: 10.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sodium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000428\n multivalued: false\n alias: sodium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soil_horizon:\n name: soil_horizon\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specific layer in the land area which measures parallel to the soil\n surface and possesses physical characteristics which differ from the layers\n above and beneath\n title: soil horizon\n examples:\n - value: A horizon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001082\n multivalued: false\n alias: soil_horizon\n owner: Biosample\n domain_of:\n - Biosample\n range: soil_horizon_enum\n soil_text_measure:\n name: soil_text_measure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to\n 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n clay loam) optional.\n title: soil texture measurement\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture measurement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000335\n multivalued: false\n alias: soil_text_measure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soil_texture_meth:\n name: soil_texture_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil texture\n title: soil texture method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000336\n multivalued: false\n alias: soil_texture_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n multivalued: false\n alias: soil_type\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n soil_type_meth:\n name: soil_type_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil series name or other\n lower-level classification\n title: soil type method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000334\n multivalued: false\n alias: soil_type_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n solar_irradiance:\n name: solar_irradiance\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per\n second\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\n title: solar irradiance\n examples:\n - value: 1.36 kilowatts per square meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solar irradiance\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000112\n multivalued: false\n alias: solar_irradiance\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soluble_inorg_mat:\n name: soluble_inorg_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as ammonia, road-salt, sea-salt,\n cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n title: soluble inorganic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble inorganic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000672\n multivalued: true\n alias: soluble_inorg_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n soluble_org_mat:\n name: soluble_org_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\n title: soluble organic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble organic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000673\n multivalued: true\n alias: soluble_org_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n soluble_react_phosp:\n name: soluble_react_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of soluble reactive phosphorus\n title: soluble reactive phosphorus\n examples:\n - value: 0.1 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble reactive phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000738\n multivalued: false\n alias: soluble_react_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000026\n multivalued: false\n alias: source_mat_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n space_typ_state:\n name: space_typ_state\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal state of the space\n title: space typical state\n examples:\n - value: typically occupied\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - space typical state\n rank: 1000\n is_a: core field\n string_serialization: '[typically occupied|typically unoccupied]'\n slot_uri: MIXS:0000770\n multivalued: false\n alias: space_typ_state\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n specific:\n name: specific\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'The building specifications. If design is chosen, indicate phase:\n conceptual, schematic, design development, construction documents'\n title: specifications\n examples:\n - value: construction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specifications\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000836\n multivalued: false\n alias: specific\n owner: Biosample\n domain_of:\n - Biosample\n range: specific_enum\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n specific_humidity:\n name: specific_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n pound.\n title: specific humidity\n examples:\n - value: 15 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specific humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000214\n multivalued: false\n alias: specific_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sr_dep_env:\n name: sr_dep_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock depositional environment\n examples:\n - value: Marine\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000996\n multivalued: false\n alias: sr_dep_env\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_dep_env_enum\n sr_geol_age:\n name: sr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000997\n multivalued: false\n alias: sr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_geol_age_enum\n sr_kerog_type:\n name: sr_kerog_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock kerogen type\n examples:\n - value: Type IV\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock kerogen type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000994\n multivalued: false\n alias: sr_kerog_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_kerog_type_enum\n sr_lithology:\n name: sr_lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock lithology\n examples:\n - value: Coal\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000995\n multivalued: false\n alias: sr_lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_lithology_enum\n standing_water_regm:\n name: standing_water_regm\n annotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to standing water during a plant's\n life span, types can be flood water or standing water, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple regimens\n title: standing water regimen\n examples:\n - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - standing water regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001069\n multivalued: true\n alias: standing_water_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n store_cond:\n name: store_cond\n annotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Explain how and for how long the soil sample was stored before DNA\n extraction (fresh/frozen/other).\n title: storage conditions\n examples:\n - value: -20 degree Celsius freezer;P2Y10D\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - storage conditions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000327\n multivalued: false\n alias: store_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n substructure_type:\n name: substructure_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The substructure or under building is that largely hidden section\n of the building which is built off the foundations to the ground floor level\n title: substructure type\n examples:\n - value: basement\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - substructure type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000767\n multivalued: true\n alias: substructure_type\n owner: Biosample\n domain_of:\n - Biosample\n range: substructure_type_enum\n sulfate:\n name: sulfate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfate in the sample\n title: sulfate\n examples:\n - value: 5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000423\n multivalued: false\n alias: sulfate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sulfate_fw:\n name: sulfate_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original sulfate concentration in the hydrocarbon resource\n title: sulfate in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000407\n multivalued: false\n alias: sulfate_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sulfide:\n name: sulfide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfide in the sample\n title: sulfide\n examples:\n - value: 2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000424\n multivalued: false\n alias: sulfide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_air_cont:\n name: surf_air_cont\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Contaminant identified on surface\n title: surface-air contaminant\n examples:\n - value: radon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface-air contaminant\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000759\n multivalued: true\n alias: surf_air_cont\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_air_cont_enum\n surf_humidity:\n name: surf_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Surfaces: water activity as a function of air and material moisture'\n title: surface humidity\n examples:\n - value: 10%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000123\n multivalued: false\n alias: surf_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_material:\n name: surf_material\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Surface materials at the point of sampling\n title: surface material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000758\n multivalued: false\n alias: surf_material\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_material_enum\n surf_moisture:\n name: surf_moisture\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Water held on a surface\n title: surface moisture\n examples:\n - value: 0.01 gram per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000128\n multivalued: false\n alias: surf_moisture\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_moisture_ph:\n name: surf_moisture_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: ph measurement of surface\n title: surface moisture pH\n examples:\n - value: '7'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000760\n multivalued: false\n alias: surf_moisture_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n surf_temp:\n name: surf_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the surface at the time of sampling\n title: surface temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000125\n multivalued: false\n alias: surf_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n suspend_part_matter:\n name: suspend_part_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of suspended particulate matter\n title: suspended particulate matter\n examples:\n - value: 0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended particulate matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000741\n multivalued: false\n alias: suspend_part_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n suspend_solids:\n name: suspend_solids\n annotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n part per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances including a wide variety of material,\n such as silt, decaying plant and animal matter; can include multiple substances\n title: suspended solids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended solids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000150\n multivalued: true\n alias: suspend_solids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tan:\n name: tan\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n title: total acid number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total acid number\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000120\n multivalued: false\n alias: tan\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n multivalued: false\n alias: target_gene\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n multivalued: false\n alias: target_subfragment\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n temp:\n name: temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n description: Temperature of the sample at the time of sampling.\n title: temperature\n examples:\n - value: 25 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000113\n multivalued: false\n alias: temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n temp_out:\n name: temp_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded temperature value at sampling time outside\n title: temperature outside house\n examples:\n - value: 5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature outside house\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000197\n multivalued: false\n alias: temp_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tertiary_treatment:\n name: tertiary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process providing a final treatment stage to raise the effluent\n quality before it is discharged to the receiving environment\n title: tertiary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tertiary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000352\n multivalued: false\n alias: tertiary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tidal_stage:\n name: tidal_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of tide\n title: tidal stage\n examples:\n - value: high tide\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tidal stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000750\n multivalued: false\n alias: tidal_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: tidal_stage_enum\n tillage:\n name: tillage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Note method(s) used for tilling\n title: history/tillage\n examples:\n - value: chisel\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/tillage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001081\n multivalued: true\n alias: tillage\n owner: Biosample\n domain_of:\n - Biosample\n range: tillage_enum\n tiss_cult_growth_med:\n name: tiss_cult_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of plant tissue culture growth media used\n title: tissue culture growth media\n examples:\n - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tissue culture growth media\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001070\n multivalued: false\n alias: tiss_cult_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n toluene:\n name: toluene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of toluene in the sample\n title: toluene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - toluene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000154\n multivalued: false\n alias: toluene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_carb:\n name: tot_carb\n description: Total carbon content\n title: total carbon\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000525\n multivalued: false\n alias: tot_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_depth_water_col:\n name: tot_depth_water_col\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of total depth of water column\n title: total depth of water column\n examples:\n - value: 500 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total depth of water column\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000634\n multivalued: false\n alias: tot_depth_water_col\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_diss_nitro:\n name: tot_diss_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n title: total dissolved nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total dissolved nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000744\n multivalued: false\n alias: tot_diss_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_inorg_nitro:\n name: tot_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total inorganic nitrogen content\n title: total inorganic nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000745\n multivalued: false\n alias: tot_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_iron:\n name: tot_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total iron in the sample\n title: total iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000105\n multivalued: false\n alias: tot_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_nitro:\n name: tot_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\n title: total nitrogen concentration\n examples:\n - value: 50 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen concentration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000102\n multivalued: false\n alias: tot_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n description: Reference or method used in determining the total nitrogen\n title: total nitrogen content method\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000338\n multivalued: false\n alias: tot_nitro_cont_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n tot_nitro_content:\n name: tot_nitro_content\n description: Total nitrogen content of the sample\n title: total nitrogen content\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000530\n multivalued: false\n alias: tot_nitro_content\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_org_c_meth:\n name: tot_org_c_meth\n description: Reference or method used in determining total organic carbon\n title: total organic carbon method\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000337\n multivalued: false\n alias: tot_org_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tot_org_carb:\n name: tot_org_carb\n description: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\n title: total organic carbon\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000533\n multivalued: false\n alias: tot_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_part_carb:\n name: tot_part_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total particulate carbon content\n title: total particulate carbon\n examples:\n - value: 35 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total particulate carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000747\n multivalued: false\n alias: tot_part_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_phosp:\n name: tot_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total phosphorus concentration in the sample, calculated by: total\n phosphorus = total dissolved phosphorus + particulate phosphorus'\n title: total phosphorus\n examples:\n - value: 0.03 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000117\n multivalued: false\n alias: tot_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_phosphate:\n name: tot_phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total amount or concentration of phosphate\n title: total phosphate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000689\n multivalued: false\n alias: tot_phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_sulfur:\n name: tot_sulfur\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total sulfur in the sample\n title: total sulfur\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total sulfur\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000419\n multivalued: false\n alias: tot_sulfur\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n train_line:\n name: train_line\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The subway line name\n title: train line\n examples:\n - value: red\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train line\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000837\n multivalued: false\n alias: train_line\n owner: Biosample\n domain_of:\n - Biosample\n range: train_line_enum\n train_stat_loc:\n name: train_stat_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train station collection location\n title: train station collection location\n examples:\n - value: forest hills\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train station collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000838\n multivalued: false\n alias: train_stat_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stat_loc_enum\n train_stop_loc:\n name: train_stop_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train stop collection location\n title: train stop collection location\n examples:\n - value: end\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train stop collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000839\n multivalued: false\n alias: train_stop_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stop_loc_enum\n turbidity:\n name: turbidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\n description: Measure of the amount of cloudiness or haziness in water caused by\n individual particles\n title: turbidity\n examples:\n - value: 0.3 nephelometric turbidity units\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - turbidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000191\n multivalued: false\n alias: turbidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tvdss_of_hcr_press:\n name: tvdss_of_hcr_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\n title: depth (TVDSS) of hydrocarbon resource pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000397\n multivalued: false\n alias: tvdss_of_hcr_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tvdss_of_hcr_temp:\n name: tvdss_of_hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\n title: depth (TVDSS) of hydrocarbon resource temperature\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000394\n multivalued: false\n alias: tvdss_of_hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n typ_occup_density:\n name: typ_occup_density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal density of occupants\n title: typical occupant density\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - typical occupant density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000771\n multivalued: false\n alias: typ_occup_density\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n ventilation_rate:\n name: ventilation_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation rate of the system in the sampled premises\n title: ventilation rate\n examples:\n - value: 750 cubic meter per minute\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000114\n multivalued: false\n alias: ventilation_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ventilation_type:\n name: ventilation_type\n annotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation system used in the sampled premises\n title: ventilation type\n examples:\n - value: Operable windows\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000756\n multivalued: false\n alias: ventilation_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n vfa:\n name: vfa\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of Volatile Fatty Acids in the sample\n title: volatile fatty acids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile fatty acids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000152\n multivalued: false\n alias: vfa\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n vfa_fw:\n name: vfa_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original volatile fatty acid concentration in the hydrocarbon resource\n title: vfa in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - vfa in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000408\n multivalued: false\n alias: vfa_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n vis_media:\n name: vis_media\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building visual media\n title: visual media\n examples:\n - value: 3D scans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - visual media\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000840\n multivalued: false\n alias: vis_media\n owner: Biosample\n domain_of:\n - Biosample\n range: vis_media_enum\n viscosity:\n name: viscosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n title: viscosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - viscosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000126\n multivalued: false\n alias: viscosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n volatile_org_comp:\n name: volatile_org_comp\n annotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of carbon-based chemicals that easily evaporate at\n room temperature; can report multiple volatile organic compounds by entering\n numeric values preceded by name of compound\n title: volatile organic compounds\n examples:\n - value: formaldehyde;500 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile organic compounds\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000115\n multivalued: true\n alias: volatile_org_comp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wall_area:\n name: wall_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The total area of the sampled room's walls\n title: wall area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000198\n multivalued: false\n alias: wall_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_const_type:\n name: wall_const_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building class of the wall defined by the composition of the\n building elements and fire-resistance rating.\n title: wall construction type\n examples:\n - value: fire resistive\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall construction type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000841\n multivalued: false\n alias: wall_const_type\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_const_type_enum\n wall_finish_mat:\n name: wall_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material utilized to finish the outer most layer of the wall\n title: wall finish material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000842\n multivalued: false\n alias: wall_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_finish_mat_enum\n wall_height:\n name: wall_height\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average height of the walls in the sampled room\n title: wall height\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000221\n multivalued: false\n alias: wall_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_loc:\n name: wall_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the wall within the room\n title: wall location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000843\n multivalued: false\n alias: wall_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_loc_enum\n wall_surf_treatment:\n name: wall_surf_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The surface treatment of interior wall\n title: wall surface treatment\n examples:\n - value: paneling\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall surface treatment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000845\n multivalued: false\n alias: wall_surf_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_surf_treatment_enum\n wall_texture:\n name: wall_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a wall surface\n title: wall texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000846\n multivalued: false\n alias: wall_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_texture_enum\n wall_thermal_mass:\n name: wall_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\n title: wall thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000222\n multivalued: false\n alias: wall_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_water_mold:\n name: wall_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a wall\n title: wall signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000844\n multivalued: false\n alias: wall_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wastewater_type:\n name: wastewater_type\n annotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\n description: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\n title: wastewater type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wastewater type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000353\n multivalued: false\n alias: wastewater_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n water_cont_soil_meth:\n name: water_cont_soil_meth\n description: Reference or method used in determining the water content of soil\n title: water content method\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000323\n multivalued: false\n alias: water_cont_soil_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n description: Water content measurement\n title: water content\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000185\n multivalued: true\n alias: water_content\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n water_current:\n name: water_current\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of magnitude and direction of flow within a fluid\n title: water current\n examples:\n - value: 10 cubic meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water current\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000203\n multivalued: false\n alias: water_current\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_cut:\n name: water_cut\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\n title: water cut\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water cut\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000454\n multivalued: false\n alias: water_cut\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_feat_size:\n name: water_feat_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the water feature\n title: water feature size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000223\n multivalued: false\n alias: water_feat_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_feat_type:\n name: water_feat_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of water feature present within the building being sampled\n title: water feature type\n examples:\n - value: stream\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000847\n multivalued: false\n alias: water_feat_type\n owner: Biosample\n domain_of:\n - Biosample\n range: water_feat_type_enum\n water_prod_rate:\n name: water_prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Water production rates per well (e.g. 987 m3 / day)\n title: water production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000453\n multivalued: false\n alias: water_prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_temp_regm:\n name: water_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple regimens\n title: water temperature regimen\n examples:\n - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000590\n multivalued: true\n alias: water_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n watering_regm:\n name: watering_regm\n description: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple regimens\n title: watering regimen\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000591\n multivalued: true\n alias: watering_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n weekday:\n name: weekday\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The day of the week when sampling occurred\n title: weekday\n examples:\n - value: Sunday\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weekday\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000848\n multivalued: false\n alias: weekday\n owner: Biosample\n domain_of:\n - Biosample\n range: weekday_enum\n win:\n name: win\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n title: well identification number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - well identification number\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000297\n multivalued: false\n alias: win\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wind_direction:\n name: wind_direction\n annotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\n description: Wind direction is the direction from which a wind originates\n title: wind direction\n examples:\n - value: Northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind direction\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000757\n multivalued: false\n alias: wind_direction\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wind_speed:\n name: wind_speed\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Speed of wind measured at the time of sampling\n title: wind speed\n examples:\n - value: 21 kilometer per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind speed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000118\n multivalued: false\n alias: wind_speed\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n window_cond:\n name: window_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the window at the time of sampling\n title: window condition\n examples:\n - value: rupture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000849\n multivalued: false\n alias: window_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cond_enum\n window_cover:\n name: window_cover\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of window covering\n title: window covering\n examples:\n - value: curtains\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window covering\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000850\n multivalued: false\n alias: window_cover\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cover_enum\n window_horiz_pos:\n name: window_horiz_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal position of the window on the wall\n title: window horizontal position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window horizontal position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000851\n multivalued: false\n alias: window_horiz_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_horiz_pos_enum\n window_loc:\n name: window_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the window within the room\n title: window location\n examples:\n - value: west\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000852\n multivalued: false\n alias: window_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: window_loc_enum\n window_mat:\n name: window_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a window\n title: window material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000853\n multivalued: false\n alias: window_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: window_mat_enum\n window_open_freq:\n name: window_open_freq\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times windows are opened per week\n title: window open frequency\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window open frequency\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000246\n multivalued: false\n alias: window_open_freq\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_size:\n name: window_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The window's length and width\n title: window area/size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window area/size\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit} x {float} {unit}'\n slot_uri: MIXS:0000224\n multivalued: false\n alias: window_size\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_status:\n name: window_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Defines whether the windows were open or closed during environmental\n testing\n title: window status\n examples:\n - value: open\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window status\n rank: 1000\n is_a: core field\n string_serialization: '[closed|open]'\n slot_uri: MIXS:0000855\n multivalued: false\n alias: window_status\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_type:\n name: window_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of windows\n title: window type\n examples:\n - value: fixed window\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000856\n multivalued: false\n alias: window_type\n owner: Biosample\n domain_of:\n - Biosample\n range: window_type_enum\n window_vert_pos:\n name: window_vert_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The vertical position of the window on the wall\n title: window vertical position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window vertical position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000857\n multivalued: false\n alias: window_vert_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_vert_pos_enum\n window_water_mold:\n name: window_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the window.\n title: window signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000854\n multivalued: false\n alias: window_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n xylene:\n name: xylene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of xylene in the sample\n title: xylene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - xylene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000156\n multivalued: false\n alias: xylene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n zinc:\n name: zinc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of zinc in the sample\n title: zinc\n examples:\n - value: 2.5 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - zinc\n rank: 1000\n is_a: attribute\n alias: zinc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n community:\n name: community\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: community\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n host_name:\n name: host_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: host_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n location:\n name: location\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: location\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n ncbi_taxonomy_name:\n name: ncbi_taxonomy_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_taxonomy_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n proport_woa_temperature:\n name: proport_woa_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: proport_woa_temperature\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n salinity_category:\n name: salinity_category\n description: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\n notes:\n - maps to gold:salinity\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-metadata/pull/297\n rank: 1000\n alias: salinity_category\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sample_collection_site:\n name: sample_collection_site\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_collection_site\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soluble_iron_micromol:\n name: soluble_iron_micromol\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: soluble_iron_micromol\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n subsurface_depth:\n name: subsurface_depth\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subsurface_depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_absorb2:\n name: dna_absorb2\n description: 260/230 measurement of DNA sample purity\n title: DNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_collect_site:\n name: dna_collect_site\n description: Provide information on the site your DNA sample was collected from\n title: DNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: dna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: dna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n dna_cont_type:\n name: dna_cont_type\n description: Tube or plate (96-well)\n title: DNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: dna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: JgiContTypeEnum\n recommended: true\n dna_container_id:\n name: dna_container_id\n title: DNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: dna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_dnase:\n name: dna_dnase\n title: DNase treatment DNA\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dna_dnase\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: YesNoEnum\n recommended: true\n dna_isolate_meth:\n name: dna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: DNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{text}'\n alias: dna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_organisms:\n name: dna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: DNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: dna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_project_contact:\n name: dna_project_contact\n title: DNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: dna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_samp_id:\n name: dna_samp_id\n title: DNA sample ID\n todos:\n - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will\n be prefilled?\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: dna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_sample_format:\n name: dna_sample_format\n description: Solution in which the DNA sample has been suspended\n title: DNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: dna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: dna_sample_format_enum\n recommended: true\n dna_sample_name:\n name: dna_sample_name\n description: Give the DNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: DNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: dna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project:\n name: dna_seq_project\n title: DNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: dna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_pi:\n name: dna_seq_project_pi\n title: DNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: dna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_name:\n name: dna_seq_project_name\n title: DNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metagenomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: dna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_volume:\n name: dna_volume\n title: DNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: dna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n proposal_dna:\n name: proposal_dna\n title: DNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_dna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dnase_rna:\n name: dnase_rna\n title: DNase treated\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dnase_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: YesNoEnum\n recommended: true\n proposal_rna:\n name: proposal_rna\n title: RNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_absorb1:\n name: rna_absorb1\n description: 260/280 measurement of RNA sample purity\n title: RNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: rna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_absorb2:\n name: rna_absorb2\n description: 260/230 measurement of RNA sample purity\n title: RNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: rna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_collect_site:\n name: rna_collect_site\n description: Provide information on the site your RNA sample was collected from\n title: RNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: rna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_concentration:\n name: rna_concentration\n title: RNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: rna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n rna_cont_type:\n name: rna_cont_type\n description: Tube or plate (96-well)\n title: RNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: rna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: JgiContTypeEnum\n recommended: true\n rna_cont_well:\n name: rna_cont_well\n title: RNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: rna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n rna_container_id:\n name: rna_container_id\n title: RNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: rna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_isolate_meth:\n name: rna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: RNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{text}'\n alias: rna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_organisms:\n name: rna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: RNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: rna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_project_contact:\n name: rna_project_contact\n title: RNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: rna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_samp_id:\n name: rna_samp_id\n title: RNA sample ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: rna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_sample_format:\n name: rna_sample_format\n description: Solution in which the RNA sample has been suspended\n title: RNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: rna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: rna_sample_format_enum\n recommended: true\n rna_sample_name:\n name: rna_sample_name\n description: Give the RNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: RNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: rna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n rna_seq_project:\n name: rna_seq_project\n title: RNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: rna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_pi:\n name: rna_seq_project_pi\n title: RNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: rna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_name:\n name: rna_seq_project_name\n title: RNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metatranscriptomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: rna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_volume:\n name: rna_volume\n title: RNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: rna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n collection_date_inc:\n name: collection_date_inc\n description: Date the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{date, arbitrary precision}'\n alias: collection_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time:\n name: collection_time\n description: The time of sampling, either as an instance (single point) or interval.\n title: collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{time, seconds optional}'\n alias: collection_time\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time_inc:\n name: collection_time_inc\n description: Time the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{time, seconds optional}'\n alias: collection_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n experimental_factor_other:\n name: experimental_factor_other\n description: Other details about your sample that you feel can't be accurately\n represented in the available columns.\n title: experimental factor- other\n comments:\n - This slot accepts open-ended text about your sample.\n - We recommend using key:value pairs.\n - Provided pairs will be considered for inclusion as future slots/terms in this\n data collection template.\n examples:\n - value: 'experimental treatment: value'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n string_serialization: '{text}'\n alias: experimental_factor_other\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n filter_method:\n name: filter_method\n description: Type of filter used or how the sample was filtered\n title: filter method\n comments:\n - describe the filter or provide a catalog number and manufacturer\n examples:\n - value: C18\n - value: Basix PES, 13-100-106 FisherSci\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{text}'\n alias: filter_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n isotope_exposure:\n name: isotope_exposure\n description: List isotope exposure or addition applied to your sample.\n title: isotope exposure/addition\n todos:\n - Can we make the H218O correctly super and subscripted?\n comments:\n - This is required when your experimental design includes the use of isotopically\n labeled compounds\n examples:\n - value: 13C glucose\n - value: H218O\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{termLabel} {[termID]}; {timestamp}'\n alias: isotope_exposure\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_c_meth:\n name: micro_biomass_c_meth\n description: Reference or method used in determining microbial biomass carbon\n title: microbial biomass carbon method\n todos:\n - How should we separate values? | or ;? lets be consistent\n comments:\n - required if \"microbial_biomass_c\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_n_meth:\n name: micro_biomass_n_meth\n description: Reference or method used in determining microbial biomass nitrogen\n title: microbial biomass nitrogen method\n comments:\n - required if \"microbial_biomass_n\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_n_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_c:\n name: microbial_biomass_c\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass carbon\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug C/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_c\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_n:\n name: microbial_biomass_n\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass nitrogen\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug N/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_n\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass:\n name: non_microb_biomass\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g.insect, plant, total. Can include multiple measurements separated\n by ;\n title: non-microbial biomass\n examples:\n - value: insect 0.23 ug; plant 1g\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n string_serialization: '{text};{float} {unit}'\n alias: non_microb_biomass\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass_method:\n name: non_microb_biomass_method\n description: Reference or method used in determining biomass\n title: non-microbial biomass method\n comments:\n - required if \"non-microbial biomass\" is provided\n examples:\n - value: https://doi.org/10.1038/s41467-021-26181-3\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: non_microb_biomass_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n org_nitro_method:\n name: org_nitro_method\n description: Method used for obtaining organic nitrogen\n title: organic nitrogen method\n comments:\n - required if \"org_nitro\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(85)90144-0\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: org_nitro_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n other_treatment:\n name: other_treatment\n description: Other treatments applied to your samples that are not applicable\n to the provided fields\n title: other treatments\n comments:\n - This is an open text field to provide any treatments that cannot be captured\n in the provided slots.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: other_treatment\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_date_inc:\n name: start_date_inc\n description: Date the incubation was started. Only relevant for incubation samples.\n title: incubation start date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{date, arbitrary precision}'\n alias: start_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_time_inc:\n name: start_time_inc\n description: Time the incubation was started. Only relevant for incubation samples.\n title: incubation start time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{time, seconds optional}'\n alias: start_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n project_id:\n name: project_id\n description: Proposal IDs or names associated with dataset\n title: project ID\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: project_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n replicate_number:\n name: replicate_number\n description: If sending biological replicates, indicate the rep number here.\n title: replicate number\n comments:\n - This will guide staff in ensuring your samples are blocked & randomized correctly\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{integer}'\n alias: replicate_number\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_shipped:\n name: sample_shipped\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample sent to EMSL.\n title: sample shipped amount\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: 15 g\n - value: 100 uL\n - value: 5 mL\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{float} {unit}'\n alias: sample_shipped\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_type:\n name: sample_type\n description: Type of sample being submitted\n title: sample type\n comments:\n - This can vary from 'environmental package' if the sample is an extraction.\n examples:\n - value: water extracted soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n alias: sample_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: sample_type_enum\n recommended: true\n technical_reps:\n name: technical_reps\n description: If sending technical replicates of the same sample, indicate the\n replicate count.\n title: number technical replicate\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{integer}'\n alias: technical_reps\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n analysis_type:\n name: analysis_type\n description: Select all the data types associated or available for this biosample\n title: analysis/data type\n examples:\n - value: metagenomics; metabolomics; proteomics\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIxS:investigation_type\n rank: 3\n multivalued: true\n alias: analysis_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: analysis_type_enum\n recommended: true\n sample_link:\n name: sample_link\n description: A unique identifier to assign parent-child, subsample, or sibling\n samples. This is relevant when a sample or other material was used to generate\n the new sample.\n title: sample linkage\n comments:\n - 'This field allows multiple entries separated by ; (Examples: Soil collected\n from the field will link with the soil used in an incubation. The soil a plant\n was grown in links to the plant sample. An original culture sample was transferred\n to a new vial and generated a new sample)'\n examples:\n - value: IGSN:DSJ0284\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{text}:{text}'\n multivalued: true\n alias: sample_link\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: string\n recommended: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Biosample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Biosample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\n notes:\n - 'id is already required to be unique because it is the identifier in Biosample''s\n parent class, NamedThing. Remember, notes like this could be exposed to end\n users. CJM suggested YAML # comment'\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nFunding-based, sample location-based, or experimental method-based defined categories
URI: BiosampleCategoryEnum
"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":"name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n LTER:\n text: LTER\n meaning: https://lternet.edu/\n title: National Science Foundation's Long Term Ecological Research Network\n SIP:\n text: SIP\n SFA:\n text: SFA\n description: Science Focus Area projects funded through the Department of Energy\n Office of Science Biological and Environmental Research Program\n meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n title: Department of Energy Office of Science Biological and Environmental Research\n Program Laboratory Science Focus Areas\n FICUS:\n text: FICUS\n meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n title: Facilities Integrating Collaborations for User Science\n NEON:\n text: NEON\n meaning: https://www.neonscience.org\n title: National Science Foundation's National Ecological Observatory Network\n\nA process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample.
URI: nmdc:BiosampleProcessing
classDiagram\n class BiosampleProcessing\n PlannedProcess <|-- BiosampleProcessing\n\n\n BiosampleProcessing <|-- Pooling\n BiosampleProcessing <|-- Extraction\n BiosampleProcessing <|-- LibraryPreparation\n\n\n BiosampleProcessing : alternative_identifiers\n\n BiosampleProcessing : description\n\n BiosampleProcessing : end_date\n\n BiosampleProcessing : has_input\n\n BiosampleProcessing --|> Biosample : has_input\n\n BiosampleProcessing : has_output\n\n BiosampleProcessing --|> NamedThing : has_output\n\n BiosampleProcessing : id\n\n BiosampleProcessing : name\n\n BiosampleProcessing : protocol_link\n\n BiosampleProcessing --|> Protocol : protocol_link\n\n BiosampleProcessing : start_date\n\n\nname: BiosampleProcessing\ndescription: A process that takes one or more biosamples as inputs and generates one\n or more biosamples as outputs. An example of an output includes samples cultivated\n from another sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- material processing\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nslots:\n- has_input\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n\nname: BiosampleProcessing\ndescription: A process that takes one or more biosamples as inputs and generates one\n or more biosamples as outputs. An example of an output includes samples cultivated\n from another sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- material processing\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: BiosampleProcessing\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: BiosampleProcessing\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: BiosampleProcessing\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: BiosampleProcessing\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: BiosampleProcessing\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: BiosampleProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: BiosampleProcessing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: BiosampleProcessing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: BiosampleProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: BioticRelationshipEnum
"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":"name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n free living:\n text: free living\n parasite:\n text: parasite\n commensal:\n text: commensal\n symbiont:\n text: symbiont\n\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
A value that is a boolean
URI: nmdc:BooleanValue
classDiagram\n class BooleanValue\n AttributeValue <|-- BooleanValue\n\n BooleanValue : has_boolean_value\n\n BooleanValue : has_raw_value\n\n BooleanValue : was_generated_by\n\n BooleanValue --|> Activity : was_generated_by\n\n\nname: BooleanValue\ndescription: A value that is a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_boolean_value\n\nname: BooleanValue\ndescription: A value that is a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_boolean_value:\n name: has_boolean_value\n description: Links a quantity value to a boolean\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: false\n alias: has_boolean_value\n owner: BooleanValue\n domain_of:\n - BooleanValue\n range: boolean\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: BooleanValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: BooleanValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: BuildDocsEnum
"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":"name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building information model:\n text: building information model\n commissioning report:\n text: commissioning report\n complaint logs:\n text: complaint logs\n contract administration:\n text: contract administration\n cost estimate:\n text: cost estimate\n janitorial schedules or logs:\n text: janitorial schedules or logs\n maintenance plans:\n text: maintenance plans\n schedule:\n text: schedule\n sections:\n text: sections\n shop drawings:\n text: shop drawings\n submittals:\n text: submittals\n ventilation system:\n text: ventilation system\n windows:\n text: windows\n\nURI: BuildOccupTypeEnum
"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":"name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n office:\n text: office\n market:\n text: market\n restaurant:\n text: restaurant\n residence:\n text: residence\n school:\n text: school\n residential:\n text: residential\n commercial:\n text: commercial\n low rise:\n text: low rise\n high rise:\n text: high rise\n wood framed:\n text: wood framed\n health care:\n text: health care\n airport:\n text: airport\n sports complex:\n text: sports complex\n\nURI: BuildingSettingEnum
"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":"name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n urban:\n text: urban\n suburban:\n text: suburban\n exurban:\n text: exurban\n rural:\n text: rural\n\nAn integer value that corresponds to a size in bytes
URI: xsd:long
base: int
uri: xsd:long
URI: CeilCondEnum
"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":"name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: CeilFinishMatEnum
"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":"name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drywall:\n text: drywall\n mineral fibre:\n text: mineral fibre\n tiles:\n text: tiles\n PVC:\n text: PVC\n plasterboard:\n text: plasterboard\n metal:\n text: metal\n fiberglass:\n text: fiberglass\n stucco:\n text: stucco\n mineral wool/calcium silicate:\n text: mineral wool/calcium silicate\n wood:\n text: wood\n\nURI: CeilTextureEnum
"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":"name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: CeilTypeEnum
"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":"name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cathedral:\n text: cathedral\n dropped:\n text: dropped\n concave:\n text: concave\n barrel-shaped:\n text: barrel-shaped\n coffered:\n text: coffered\n cove:\n text: cove\n stretched:\n text: stretched\n\nA MIxS checklist. These can be combined with packages
URI: Checklist
"},{"location":"Checklist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Checklist/#schema-source","title":"Schema Source","text":"A combination of a checklist and a package
URI: ChecklistPackageCombination
"},{"location":"ChecklistPackageCombination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChecklistPackageCombination/#schema-source","title":"Schema Source","text":"An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states
URI: nmdc:ChemicalEntity
classDiagram\n class ChemicalEntity\n OntologyClass <|-- ChemicalEntity\n\n ChemicalEntity : alternative_identifiers\n\n ChemicalEntity : chemical_formula\n\n ChemicalEntity : description\n\n ChemicalEntity : id\n\n ChemicalEntity : inchi\n\n ChemicalEntity : inchi_key\n\n ChemicalEntity : name\n\n ChemicalEntity : smiles\n\n\nInstances of this class should have identifiers with one of the following prefixes:
cas
CHEBI
CHEMBL.COMPOUND
DRUGBANK
HMDB
KEGG.COMPOUND
MESH
PUBCHEM.COMPOUND
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- chemical_formula\n- inchi\n- inchi_key\n- smiles\n\nname: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n chemical_formula:\n name: chemical_formula\n description: A generic grouping for molecular formulae and empirical formulae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_formula\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n inchi:\n name: inchi\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: inchi\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n inchi_key:\n name: inchi_key\n notes:\n - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: inchi_key\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n smiles:\n name: smiles\n description: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: smiles\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalEntity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalEntity\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: ChemicalEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:CollectingBiosamplesFromSite
classDiagram\n class CollectingBiosamplesFromSite\n PlannedProcess <|-- CollectingBiosamplesFromSite\n\n CollectingBiosamplesFromSite : alternative_identifiers\n\n CollectingBiosamplesFromSite : description\n\n CollectingBiosamplesFromSite : end_date\n\n CollectingBiosamplesFromSite : has_input\n\n CollectingBiosamplesFromSite --|> Site : has_input\n\n CollectingBiosamplesFromSite : has_output\n\n CollectingBiosamplesFromSite --|> Biosample : has_output\n\n CollectingBiosamplesFromSite : id\n\n CollectingBiosamplesFromSite : name\n\n CollectingBiosamplesFromSite : protocol_link\n\n CollectingBiosamplesFromSite --|> Protocol : protocol_link\n\n CollectingBiosamplesFromSite : start_date\n\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: CollectingBiosamplesFromSite\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: CollectingBiosamplesFromSite\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ContainerTypeEnum
"},{"location":"ContainerTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description screw_top_conical None"},{"location":"ContainerTypeEnum/#slots","title":"Slots","text":"Name Description container_type"},{"location":"ContainerTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerTypeEnum/#schema-source","title":"Schema Source","text":"name: ContainerTypeEnum\ntitle: Container type enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n screw_top_conical:\n text: screw_top_conical\n title: Screw top conical tube\n aliases:\n - falcon tube\n\nA controlled term or class from an ontology, requiring the presence of term with an id
URI: nmdc:ControlledIdentifiedTermValue
classDiagram\n class ControlledIdentifiedTermValue\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n\n ControlledIdentifiedTermValue : has_raw_value\n\n ControlledIdentifiedTermValue : term\n\n ControlledIdentifiedTermValue --|> OntologyClass : term\n\n ControlledIdentifiedTermValue : was_generated_by\n\n ControlledIdentifiedTermValue --|> Activity : was_generated_by\n\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n domain_of:\n - ControlledTermValue\n required: true\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n domain_of:\n - ControlledTermValue\n required: true\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: ControlledTermValue\n alias: term\n owner: ControlledIdentifiedTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n required: true\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ControlledIdentifiedTermValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ControlledIdentifiedTermValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nA controlled term or class from an ontology
URI: nmdc:ControlledTermValue
classDiagram\n class ControlledTermValue\n AttributeValue <|-- ControlledTermValue\n\n\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n\n\n ControlledTermValue : has_raw_value\n\n ControlledTermValue : term\n\n ControlledTermValue --|> OntologyClass : term\n\n ControlledTermValue : was_generated_by\n\n ControlledTermValue --|> Activity : was_generated_by\n\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: ControlledTermValue\n alias: term\n owner: ControlledTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ControlledTermValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ControlledTermValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nThis class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0
URI: prov:Association
classDiagram\n class CreditAssociation\n CreditAssociation : applied_role\n\n CreditAssociation --|> credit enum : applied_role\n\n CreditAssociation : applied_roles\n\n CreditAssociation --|> credit enum : applied_roles\n\n CreditAssociation : applies_to_person\n\n CreditAssociation --|> PersonValue : applies_to_person\n\n CreditAssociation : type\n\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/)\n and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_role\n- applied_roles\n- type\nclass_uri: prov:Association\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/)\n and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n applies_to_person:\n name: applies_to_person\n todos:\n - prov:agent takes an Agent object. Is a person value an Agent? Also try to relate\n to principal investigator slot? could include OBI:0000103 principal investigator\n role... do we need to define the OBI prefix?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n alias: applies_to_person\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: PersonValue\n required: true\n applied_role:\n name: applied_role\n deprecated: A credit association may have multiple roles. So, use the applied\n roles slot.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n slot_uri: prov:hadRole\n alias: applied_role\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: credit enum\n applied_roles:\n name: applied_roles\n annotations:\n display_hint:\n tag: display_hint\n value: 'Identify all CRediT roles associated with this contributor. CRediT\n Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n https://credit.niso.org/'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n multivalued: true\n alias: applied_roles\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: credit enum\n required: true\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: CreditAssociation\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\nclass_uri: prov:Association\n\nURI: CreditEnum
"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_role applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":"name: credit enum\ncomments:\n- credit enums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Conceptualization:\n text: Conceptualization\n description: Conceptualization\n Data curation:\n text: Data curation\n description: Data curation\n Formal Analysis:\n text: Formal Analysis\n description: Formal Analysis\n Funding acquisition:\n text: Funding acquisition\n description: Funding acquisition\n Investigation:\n text: Investigation\n description: Investigation\n Methodology:\n text: Methodology\n description: Methodology\n Project administration:\n text: Project administration\n description: Project administration\n Resources:\n text: Resources\n description: Resources\n Software:\n text: Software\n description: Software\n Supervision:\n text: Supervision\n description: Supervision\n Validation:\n text: Validation\n description: Validation\n Visualization:\n text: Visualization\n description: Visualization\n Writing original draft:\n text: Writing original draft\n description: Writing \u2013 original draft\n Writing review and editing:\n text: Writing review and editing\n description: Writing \u2013 review & editing\n Principal Investigator:\n text: Principal Investigator\n description: principal investigator role\n meaning: OBI:0000103\n Submitter:\n text: Submitter\n description: the person(s) who enter study and biosample metadata into the NMDC\n submission portal\n meaning: EFO:0001741\n\nURI: CurLandUseEnum
"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":"name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n badlands:\n text: badlands\n cities:\n text: cities\n conifers:\n text: conifers\n annotations:\n originally:\n tag: originally\n value: conifers (e.g. pine,spruce,fir,cypress)\n examples:\n - value: cypress\n - value: fir\n - value: pine\n - value: spruce\n crop trees:\n text: crop trees\n annotations:\n originally:\n tag: originally\n value: crop trees (nuts,fruit,christmas trees,nursery trees)\n examples:\n - value: christmas trees\n - value: fruit\n - value: nursery trees\n - value: nuts\n farmstead:\n text: farmstead\n gravel:\n text: gravel\n hardwoods:\n text: hardwoods\n annotations:\n originally:\n tag: originally\n value: hardwoods (e.g. oak,hickory,elm,aspen)\n examples:\n - value: aspen\n - value: elm\n - value: hickory\n - value: oak\n hayland:\n text: hayland\n horticultural plants:\n text: horticultural plants\n annotations:\n originally:\n tag: originally\n value: horticultural plants (e.g. tulips)\n examples:\n - value: tulips\n industrial areas:\n text: industrial areas\n intermixed hardwood and conifers:\n text: intermixed hardwood and conifers\n marshlands:\n text: marshlands\n annotations:\n originally:\n tag: originally\n value: marshlands (grass,sedges,rushes)\n examples:\n - value: grass\n - value: rushes\n - value: sedgees\n meadows:\n text: meadows\n annotations:\n originally:\n tag: originally\n value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n examples:\n - value: alfalfa\n - value: bromegrass\n - value: fescue\n - value: grasses\n - value: timothy\n mines/quarries:\n text: mines/quarries\n mudflats:\n text: mudflats\n oil waste areas:\n text: oil waste areas\n pastureland:\n text: pastureland\n annotations:\n originally:\n tag: originally\n value: pastureland (grasslands used for livestock grazing)\n comments:\n - grasslands used for livestock grazing\n permanent snow or ice:\n text: permanent snow or ice\n rainforest:\n text: rainforest\n annotations:\n originally:\n tag: originally\n value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n comments:\n - evergreen forest receiving greater than 406 cm annual rainfall\n rangeland:\n text: rangeland\n roads/railroads:\n text: roads/railroads\n rock:\n text: rock\n row crops:\n text: row crops\n saline seeps:\n text: saline seeps\n salt flats:\n text: salt flats\n sand:\n text: sand\n shrub crops:\n text: shrub crops\n annotations:\n originally:\n tag: originally\n value: shrub crops (blueberries,nursery ornamentals,filberts)\n examples:\n - value: blueberries\n - value: filberts\n - value: nursery ornamentals\n shrub land:\n text: shrub land\n annotations:\n originally:\n tag: originally\n value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n examples:\n - value: creosote bush\n - value: eucalyptus\n - value: mesquite\n - value: sage-brush\n - value: shrub oak\n small grains:\n text: small grains\n successional shrub land:\n text: successional shrub land\n annotations:\n originally:\n tag: originally\n value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n dogwoods,blackberries)\n examples:\n - value: blackberries\n - value: chokecherry\n - value: hazels\n - value: shrub dogwoods\n - value: sumacs\n - value: tree saplings\n swamp:\n text: swamp\n annotations:\n originally:\n tag: originally\n value: swamp (permanent or semi-permanent water body dominated by woody plants)\n comments:\n - permanent or semi-permanent water body dominated by woody plants\n tropical:\n text: tropical\n annotations:\n originally:\n tag: originally\n value: tropical (e.g. mangrove,palms)\n examples:\n - value: mangrove\n - value: palms\n tundra:\n text: tundra\n annotations:\n originally:\n tag: originally\n value: tundra (mosses,lichens)\n examples:\n - value: lichens\n - value: mosses\n vegetable crops:\n text: vegetable crops\n vine crops:\n text: vine crops\n annotations:\n originally:\n tag: originally\n value: vine crops (grapes)\n examples:\n - value: grapes\n\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
URI: nmdc:DataObject
classDiagram\n class DataObject\n NamedThing <|-- DataObject\n\n DataObject : alternative_identifiers\n\n DataObject : compression_type\n\n DataObject : data_object_type\n\n DataObject --|> file type enum : data_object_type\n\n DataObject : description\n\n DataObject : file_size_bytes\n\n DataObject : id\n\n DataObject : md5_checksum\n\n DataObject : name\n\n DataObject : type\n\n DataObject : url\n\n DataObject : was_generated_by\n\n DataObject --|> Activity : was_generated_by\n\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\ncomments:\n- removed id_prefixes value of GOLD, since we are now using pattern-based id validation\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslots:\n- file_size_bytes\n- md5_checksum\n- data_object_type\n- compression_type\n- was_generated_by\n- url\n- type\nslot_usage:\n name:\n name: name\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n required: true\n description:\n name: description\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\ncomments:\n- removed id_prefixes value of GOLD, since we are now using pattern-based id validation\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n name:\n name: name\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n required: true\n description:\n name: description\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n file_size_bytes:\n name: file_size_bytes\n description: Size of the file in bytes\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: file_size_bytes\n owner: DataObject\n domain_of:\n - DataObject\n range: bytes\n md5_checksum:\n name: md5_checksum\n description: MD5 checksum of file (pre-compressed)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: md5_checksum\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n data_object_type:\n name: data_object_type\n description: The type of file represented by the data object.\n examples:\n - value: FT ICR-MS Analysis Results\n - value: GC-MS Metabolomics Results\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: data_object_type\n owner: DataObject\n domain_of:\n - DataObject\n range: file type enum\n compression_type:\n name: compression_type\n description: If provided, specifies the compression type\n todos:\n - consider enum\n examples:\n - value: gzip\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: compression_type\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: DataObject\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: DataObject\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: DataObject\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: DataObject\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataObject\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataObject\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: DataObject\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSubset consisting of the data objects that either inputs or outputs of processes or workflows.
URI: DataObjectSubset
"},{"location":"DataObjectSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObjectSubset/#schema-source","title":"Schema Source","text":"An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
"},{"location":"Database/","title":"Class: Database","text":"An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest
URI: nmdc:Database
classDiagram\n class Database\n Database : activity_set\n\n Database --|> WorkflowExecutionActivity : activity_set\n\n Database : biosample_set\n\n Database --|> Biosample : biosample_set\n\n Database : collecting_biosamples_from_site_set\n\n Database --|> CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n\n Database : data_object_set\n\n Database --|> DataObject : data_object_set\n\n Database : date_created\n\n Database : dissolving_activity_set\n\n Database --|> DissolvingActivity : dissolving_activity_set\n\n Database : etl_software_version\n\n Database : extraction_set\n\n Database --|> Extraction : extraction_set\n\n Database : field_research_site_set\n\n Database --|> FieldResearchSite : field_research_site_set\n\n Database : functional_annotation_agg\n\n Database --|> FunctionalAnnotationAggMember : functional_annotation_agg\n\n Database : functional_annotation_set\n\n Database --|> FunctionalAnnotation : functional_annotation_set\n\n Database : genome_feature_set\n\n Database --|> GenomeFeature : genome_feature_set\n\n Database : library_preparation_set\n\n Database --|> LibraryPreparation : library_preparation_set\n\n Database : mags_activity_set\n\n Database --|> MagsAnalysisActivity : mags_activity_set\n\n Database : material_sample_set\n\n Database --|> MaterialSample : material_sample_set\n\n Database : material_sampling_activity_set\n\n Database --|> MaterialSamplingActivity : material_sampling_activity_set\n\n Database : metabolomics_analysis_activity_set\n\n Database --|> MetabolomicsAnalysisActivity : metabolomics_analysis_activity_set\n\n Database : metagenome_annotation_activity_set\n\n Database --|> MetagenomeAnnotationActivity : metagenome_annotation_activity_set\n\n Database : metagenome_assembly_set\n\n Database --|> MetagenomeAssembly : metagenome_assembly_set\n\n Database : metagenome_sequencing_activity_set\n\n Database --|> MetagenomeSequencingActivity : metagenome_sequencing_activity_set\n\n Database : metaproteomics_analysis_activity_set\n\n Database --|> MetaproteomicsAnalysisActivity : metaproteomics_analysis_activity_set\n\n Database : metatranscriptome_activity_set\n\n Database --|> MetatranscriptomeActivity : metatranscriptome_activity_set\n\n Database : nom_analysis_activity_set\n\n Database --|> NomAnalysisActivity : nom_analysis_activity_set\n\n Database : omics_processing_set\n\n Database --|> OmicsProcessing : omics_processing_set\n\n Database : pooling_set\n\n Database --|> Pooling : pooling_set\n\n Database : processed_sample_set\n\n Database --|> ProcessedSample : processed_sample_set\n\n Database : reaction_activity_set\n\n Database --|> ReactionActivity : reaction_activity_set\n\n Database : read_based_taxonomy_analysis_activity_set\n\n Database --|> ReadBasedTaxonomyAnalysisActivity : read_based_taxonomy_analysis_activity_set\n\n Database : read_qc_analysis_activity_set\n\n Database --|> ReadQcAnalysisActivity : read_qc_analysis_activity_set\n\n Database : study_set\n\n Database --|> Study : study_set\n\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- functional_annotation_agg\n- library_preparation_set\n- processed_sample_set\n- extraction_set\n- activity_set\n- biosample_set\n- data_object_set\n- dissolving_activity_set\n- functional_annotation_set\n- genome_feature_set\n- mags_activity_set\n- material_sample_set\n- material_sampling_activity_set\n- metabolomics_analysis_activity_set\n- metagenome_annotation_activity_set\n- metagenome_assembly_set\n- metagenome_sequencing_activity_set\n- metaproteomics_analysis_activity_set\n- metatranscriptome_activity_set\n- nom_analysis_activity_set\n- omics_processing_set\n- reaction_activity_set\n- read_qc_analysis_activity_set\n- read_based_taxonomy_analysis_activity_set\n- study_set\n- field_research_site_set\n- collecting_biosamples_from_site_set\n- date_created\n- etl_software_version\n- metatranscriptome_activity_set\n- pooling_set\n- extraction_set\nslot_usage:\n date_created:\n name: date_created\n todos:\n - description\n domain_of:\n - Database\n etl_software_version:\n name: etl_software_version\n todos:\n - description\n domain_of:\n - Database\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n todos:\n - description\n domain_of:\n - Database\ntree_root: true\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslot_usage:\n date_created:\n name: date_created\n todos:\n - description\n domain_of:\n - Database\n etl_software_version:\n name: etl_software_version\n todos:\n - description\n domain_of:\n - Database\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n todos:\n - description\n domain_of:\n - Database\nattributes:\n functional_annotation_agg:\n name: functional_annotation_agg\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: functional_annotation_agg\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotationAggMember\n inlined: true\n inlined_as_list: true\n library_preparation_set:\n name: library_preparation_set\n description: This property links a database object to the set of DNA extractions\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - library_construction_set\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: library_preparation_set\n owner: Database\n domain_of:\n - Database\n range: LibraryPreparation\n inlined_as_list: true\n processed_sample_set:\n name: processed_sample_set\n description: This property links a database object to the set of processed samples\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: processed_sample_set\n owner: Database\n domain_of:\n - Database\n range: ProcessedSample\n inlined_as_list: true\n extraction_set:\n name: extraction_set\n description: This property links a database object to the set of extractions within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: extraction_set\n owner: Database\n domain_of:\n - Database\n range: Extraction\n inlined_as_list: true\n activity_set:\n name: activity_set\n description: This property links a database object to the set of workflow activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: activity_set\n owner: Database\n domain_of:\n - Database\n range: WorkflowExecutionActivity\n inlined_as_list: true\n biosample_set:\n name: biosample_set\n description: This property links a database object to the set of samples within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: biosample_set\n owner: Database\n domain_of:\n - Database\n range: Biosample\n inlined_as_list: true\n data_object_set:\n name: data_object_set\n description: This property links a database object to the set of data objects\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: data_object_set\n owner: Database\n domain_of:\n - Database\n range: DataObject\n inlined_as_list: true\n dissolving_activity_set:\n name: dissolving_activity_set\n title: dissolving activity set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: dissolving_activity_set\n owner: Database\n domain_of:\n - Database\n range: DissolvingActivity\n inlined: true\n inlined_as_list: true\n functional_annotation_set:\n name: functional_annotation_set\n description: This property links a database object to the set of all functional\n annotations\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: functional_annotation_set\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotation\n inlined_as_list: true\n genome_feature_set:\n name: genome_feature_set\n description: This property links a database object to the set of all features\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: genome_feature_set\n owner: Database\n domain_of:\n - Database\n range: GenomeFeature\n inlined_as_list: true\n mags_activity_set:\n name: mags_activity_set\n description: This property links a database object to the set of MAGs analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: mags_activity_set\n owner: Database\n domain_of:\n - Database\n range: MagsAnalysisActivity\n inlined_as_list: true\n material_sample_set:\n name: material_sample_set\n title: material sample set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: material_sample_set\n owner: Database\n domain_of:\n - Database\n range: MaterialSample\n inlined: true\n inlined_as_list: true\n material_sampling_activity_set:\n name: material_sampling_activity_set\n title: material sampling activity set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: material_sampling_activity_set\n owner: Database\n domain_of:\n - Database\n range: MaterialSamplingActivity\n inlined: true\n inlined_as_list: true\n metabolomics_analysis_activity_set:\n name: metabolomics_analysis_activity_set\n description: This property links a database object to the set of metabolomics\n analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metabolomics_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetabolomicsAnalysisActivity\n inlined_as_list: true\n metagenome_annotation_activity_set:\n name: metagenome_annotation_activity_set\n description: This property links a database object to the set of metagenome annotation\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_annotation_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeAnnotationActivity\n inlined_as_list: true\n metagenome_assembly_set:\n name: metagenome_assembly_set\n description: This property links a database object to the set of metagenome assembly\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_assembly_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeAssembly\n inlined_as_list: true\n metagenome_sequencing_activity_set:\n name: metagenome_sequencing_activity_set\n description: This property links a database object to the set of metagenome sequencing\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_sequencing_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeSequencingActivity\n inlined_as_list: true\n metaproteomics_analysis_activity_set:\n name: metaproteomics_analysis_activity_set\n description: This property links a database object to the set of metaproteomics\n analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metaproteomics_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetaproteomicsAnalysisActivity\n inlined_as_list: true\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n description: This property links a database object to the set of metatranscriptome\n analysis activities.\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: metatranscriptome_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetatranscriptomeActivity\n inlined_as_list: true\n nom_analysis_activity_set:\n name: nom_analysis_activity_set\n description: This property links a database object to the set of natural organic\n matter (NOM) analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: nom_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: NomAnalysisActivity\n inlined_as_list: true\n omics_processing_set:\n name: omics_processing_set\n description: This property links a database object to the set of omics processings\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: omics_processing_set\n owner: Database\n domain_of:\n - Database\n range: OmicsProcessing\n inlined_as_list: true\n reaction_activity_set:\n name: reaction_activity_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: reaction_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReactionActivity\n inlined: true\n inlined_as_list: true\n read_qc_analysis_activity_set:\n name: read_qc_analysis_activity_set\n description: This property links a database object to the set of read QC analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: read_qc_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReadQcAnalysisActivity\n inlined_as_list: true\n read_based_taxonomy_analysis_activity_set:\n name: read_based_taxonomy_analysis_activity_set\n description: This property links a database object to the set of read based analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: read_based_taxonomy_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReadBasedTaxonomyAnalysisActivity\n inlined_as_list: true\n study_set:\n name: study_set\n description: This property links a database object to the set of studies within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: study_set\n owner: Database\n domain_of:\n - Database\n range: Study\n inlined_as_list: true\n field_research_site_set:\n name: field_research_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: field_research_site_set\n owner: Database\n domain_of:\n - Database\n range: FieldResearchSite\n inlined: true\n inlined_as_list: true\n collecting_biosamples_from_site_set:\n name: collecting_biosamples_from_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: collecting_biosamples_from_site_set\n owner: Database\n domain_of:\n - Database\n range: CollectingBiosamplesFromSite\n inlined: true\n inlined_as_list: true\n date_created:\n name: date_created\n description: from database class\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: date_created\n owner: Database\n domain_of:\n - Database\n range: string\n etl_software_version:\n name: etl_software_version\n description: from database class\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: etl_software_version\n owner: Database\n domain_of:\n - Database\n range: string\n pooling_set:\n name: pooling_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: pooling_set\n owner: Database\n domain_of:\n - Database\n range: Pooling\n inlined_as_list: true\ntree_root: true\n\na date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
A decimal degree expresses latitude or longitude as decimal fractions.
URI: xsd:decimal
base: float
uri: xsd:decimal
URI: DeposEnvEnum
"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":"name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Continental - Alluvial:\n text: Continental - Alluvial\n Continental - Aeolian:\n text: Continental - Aeolian\n Continental - Fluvial:\n text: Continental - Fluvial\n Continental - Lacustrine:\n text: Continental - Lacustrine\n Transitional - Deltaic:\n text: Transitional - Deltaic\n Transitional - Tidal:\n text: Transitional - Tidal\n Transitional - Lagoonal:\n text: Transitional - Lagoonal\n Transitional - Beach:\n text: Transitional - Beach\n Transitional - Lake:\n text: Transitional - Lake\n Marine - Shallow:\n text: Marine - Shallow\n Marine - Deep:\n text: Marine - Deep\n Marine - Reef:\n text: Marine - Reef\n Other - Evaporite:\n text: Other - Evaporite\n Other - Glacial:\n text: Other - Glacial\n Other - Volcanic:\n text: Other - Volcanic\n other:\n text: other\n\nURI: DeviceTypeEnum
"},{"location":"DeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description orbital_shaker None thermomixer None"},{"location":"DeviceTypeEnum/#slots","title":"Slots","text":"Name Description device_type"},{"location":"DeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: DeviceTypeEnum\ntitle: Shaker type enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n orbital_shaker:\n text: orbital_shaker\n title: Orbital shaker\n thermomixer:\n text: thermomixer\n title: Thermomixer\n\nURI: CHMO:0002773
classDiagram\n class DissolvingActivity\n DissolvingActivity : dissolution_aided_by\n\n DissolvingActivity --|> LabDevice : dissolution_aided_by\n\n DissolvingActivity : dissolution_reagent\n\n DissolvingActivity --|> SolventEnum : dissolution_reagent\n\n DissolvingActivity : dissolution_volume\n\n DissolvingActivity --|> QuantityValue : dissolution_volume\n\n DissolvingActivity : dissolved_in\n\n DissolvingActivity --|> MaterialContainer : dissolved_in\n\n DissolvingActivity : material_input\n\n DissolvingActivity --|> MaterialSample : material_input\n\n DissolvingActivity : material_output\n\n DissolvingActivity --|> MaterialSample : material_output\n\n\nname: DissolvingActivity\ntitle: Dissolving activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolution-activity\nslots:\n- dissolution_aided_by\n- dissolution_reagent\n- dissolution_volume\n- dissolved_in\n- material_input\n- material_output\nslot_usage:\n material_input:\n name: material_input\n examples:\n - value: somextract:6\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:7\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nclass_uri: CHMO:0002773\n\nname: DissolvingActivity\ntitle: Dissolving activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolution-activity\nslot_usage:\n material_input:\n name: material_input\n examples:\n - value: somextract:6\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:7\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nattributes:\n dissolution_aided_by:\n name: dissolution_aided_by\n title: dissolution aided by\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker\n rank: 1000\n alias: dissolution_aided_by\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: LabDevice\n inlined: true\n dissolution_reagent:\n name: dissolution_reagent\n title: dissolution reagent\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solvent\n rank: 1000\n alias: dissolution_reagent\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: SolventEnum\n dissolution_volume:\n name: dissolution_volume\n title: dissolution volume\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volume\n rank: 1000\n alias: dissolution_volume\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: QuantityValue\n inlined: true\n dissolved_in:\n name: dissolved_in\n title: dissolved in\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - container\n rank: 1000\n alias: dissolved_in\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: MaterialContainer\n inlined: true\n material_input:\n name: material_input\n title: material input\n examples:\n - value: somextract:6\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_input\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n range: MaterialSample\n material_output:\n name: material_output\n title: material output\n examples:\n - value: somextract:7\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_output\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\nclass_uri: CHMO:0002773\n\nURI: DnaSampleFormatEnum
"},{"location":"DnaSampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DnaSampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DnaSampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DnaSampleFormatEnum/#schema-source","title":"Schema Source","text":"name: dna_sample_format_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: DoorCompTypeEnum
"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":"name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metal covered:\n text: metal covered\n revolving:\n text: revolving\n sliding:\n text: sliding\n telescopic:\n text: telescopic\n\nURI: DoorCondEnum
"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":"name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: DoorDirectEnum
"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":"name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n inward:\n text: inward\n outward:\n text: outward\n sideways:\n text: sideways\n\nURI: DoorLocEnum
"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":"name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: DoorMatEnum
"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":"name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aluminum:\n text: aluminum\n cellular PVC:\n text: cellular PVC\n engineered plastic:\n text: engineered plastic\n fiberboard:\n text: fiberboard\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n thermoplastic alloy:\n text: thermoplastic alloy\n vinyl:\n text: vinyl\n wood:\n text: wood\n wood/plastic composite:\n text: wood/plastic composite\n\nURI: DoorMoveEnum
"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":"name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n folding:\n text: folding\n revolving:\n text: revolving\n rolling shutter:\n text: rolling shutter\n sliding:\n text: sliding\n swinging:\n text: swinging\n\nURI: DoorTypeEnum
"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":"name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n composite:\n text: composite\n metal:\n text: metal\n wooden:\n text: wooden\n\nURI: DoorTypeMetalEnum
"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":"name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n corrugated steel:\n text: corrugated steel\n hollow:\n text: hollow\n rolling shutters:\n text: rolling shutters\n steel plate:\n text: steel plate\n\nURI: DoorTypeWoodEnum
"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":"name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bettened and ledged:\n text: bettened and ledged\n battened:\n text: battened\n ledged and braced:\n text: ledged and braced\n ledged and framed:\n text: ledged and framed\n ledged, braced and frame:\n text: ledged, braced and frame\n framed and paneled:\n text: framed and paneled\n glashed or sash:\n text: glashed or sash\n flush:\n text: flush\n louvered:\n text: louvered\n wire gauged:\n text: wire gauged\n\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
URI: DrainageClassEnum
"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":"name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n very poorly:\n text: very poorly\n poorly:\n text: poorly\n somewhat poorly:\n text: somewhat poorly\n moderately well:\n text: moderately well\n well:\n text: well\n excessively drained:\n text: excessively drained\n\nURI: DrawingsEnum
"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":"name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n building navigation map:\n text: building navigation map\n diagram:\n text: diagram\n sketch:\n text: sketch\n\nURI: Environment
"},{"location":"Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Environment/#schema-source","title":"Schema Source","text":"URI: nmdc:EnvironmentalMaterialTerm
classDiagram\n class EnvironmentalMaterialTerm\n OntologyClass <|-- EnvironmentalMaterialTerm\n\n EnvironmentalMaterialTerm : alternative_identifiers\n\n EnvironmentalMaterialTerm : description\n\n EnvironmentalMaterialTerm : id\n\n EnvironmentalMaterialTerm : name\n\n\nname: EnvironmentalMaterialTerm\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\n\nname: EnvironmentalMaterialTerm\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ExtWallOrientEnum
"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nURI: ExtWindowOrientEnum
"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nA CURIE representing an external identifier
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
typeof: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
A material separation in which a desired component of an input material is separated from the remainder.
URI: nmdc:Extraction
classDiagram\n class Extraction\n BiosampleProcessing <|-- Extraction\n\n Extraction : alternative_identifiers\n\n Extraction : description\n\n Extraction : end_date\n\n Extraction : extraction_method\n\n Extraction : extraction_target\n\n Extraction --|> ExtractionTargetEnum : extraction_target\n\n Extraction : has_input\n\n Extraction --|> Biosample : has_input\n\n Extraction : has_output\n\n Extraction --|> NamedThing : has_output\n\n Extraction : id\n\n Extraction : input_mass\n\n Extraction --|> QuantityValue : input_mass\n\n Extraction : name\n\n Extraction : processing_institution\n\n Extraction --|> processing_institution_enum : processing_institution\n\n Extraction : protocol_link\n\n Extraction --|> Protocol : protocol_link\n\n Extraction : quality_control_report\n\n Extraction --|> QualityControlReport : quality_control_report\n\n Extraction : start_date\n\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: BiosampleProcessing\nslots:\n- extraction_method\n- extraction_target\n- processing_institution\n- protocol_link\n- quality_control_report\n- input_mass\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n extraction_method:\n name: extraction_method\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: extraction_method\n owner: Extraction\n domain_of:\n - Extraction\n range: string\n extraction_target:\n name: extraction_target\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: extraction_target\n owner: Extraction\n domain_of:\n - Extraction\n range: ExtractionTargetEnum\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Extraction\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Extraction\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n quality_control_report:\n name: quality_control_report\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: quality_control_report\n owner: Extraction\n domain_of:\n - Extraction\n range: QualityControlReport\n input_mass:\n name: input_mass\n description: Total mass of sample used in activity.\n title: sample mass used\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample mass\n - sample weight\n exact_mappings:\n - MS:1000004\n rank: 1000\n alias: input_mass\n owner: Extraction\n domain_of:\n - Extraction\n range: QuantityValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: Extraction\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: Extraction\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Extraction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Extraction\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Extraction\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Extraction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ExtractionTargetEnum
"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_target"},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":"name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n metabolite:\n text: metabolite\n protein:\n text: protein\n\nURI: FaoClassEnum
"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":"name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Acrisols:\n text: Acrisols\n Andosols:\n text: Andosols\n Arenosols:\n text: Arenosols\n Cambisols:\n text: Cambisols\n Chernozems:\n text: Chernozems\n Ferralsols:\n text: Ferralsols\n Fluvisols:\n text: Fluvisols\n Gleysols:\n text: Gleysols\n Greyzems:\n text: Greyzems\n Gypsisols:\n text: Gypsisols\n Histosols:\n text: Histosols\n Kastanozems:\n text: Kastanozems\n Lithosols:\n text: Lithosols\n Luvisols:\n text: Luvisols\n Nitosols:\n text: Nitosols\n Phaeozems:\n text: Phaeozems\n Planosols:\n text: Planosols\n Podzols:\n text: Podzols\n Podzoluvisols:\n text: Podzoluvisols\n Rankers:\n text: Rankers\n Regosols:\n text: Regosols\n Rendzinas:\n text: Rendzinas\n Solonchaks:\n text: Solonchaks\n Solonetz:\n text: Solonetz\n Vertisols:\n text: Vertisols\n Yermosols:\n text: Yermosols\n\nA site, outside of a laboratory, from which biosamples may be collected.
URI: nmdc:FieldResearchSite
classDiagram\n class FieldResearchSite\n Site <|-- FieldResearchSite\n\n FieldResearchSite : alternative_identifiers\n\n FieldResearchSite : cur_vegetation\n\n FieldResearchSite --|> TextValue : cur_vegetation\n\n FieldResearchSite : description\n\n FieldResearchSite : elev\n\n FieldResearchSite --|> QuantityValue : elev\n\n FieldResearchSite : geo_loc_name\n\n FieldResearchSite --|> TextValue : geo_loc_name\n\n FieldResearchSite : habitat\n\n FieldResearchSite : id\n\n FieldResearchSite : lat_lon\n\n FieldResearchSite --|> GeolocationValue : lat_lon\n\n FieldResearchSite : local_class\n\n FieldResearchSite --|> TextValue : local_class\n\n FieldResearchSite : name\n\n FieldResearchSite : part_of\n\n FieldResearchSite --|> NamedThing : part_of\n\n FieldResearchSite : soil_type\n\n FieldResearchSite --|> TextValue : soil_type\n\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n multivalued: false\n alias: cur_vegetation\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n multivalued: false\n alias: elev\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: QuantityValue\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n multivalued: false\n alias: geo_loc_name\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n multivalued: false\n alias: lat_lon\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n multivalued: false\n alias: local_class\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n multivalued: false\n alias: soil_type\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: FieldResearchSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FieldResearchSite\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FieldResearchSite\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: FieldResearchSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: FileTypeEnum
"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Metagenome Raw Reads None Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome Bins Compression File None Compressed file containing all metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... Raw Compressed Metagenome Interleaved Paired-End Reads None Raw sequencing reads from a metagenome that is in interleaved paired-end form..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":"name: file type enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Metagenome Raw Reads:\n text: Metagenome Raw Reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^\\.fastq(\\.gz)?$\n Metagenome Raw Read 1:\n text: Metagenome Raw Read 1\n description: Read 1 raw sequencing data, aka forward reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R1\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n Metagenome Raw Read 2:\n text: Metagenome Raw Read 2\n description: Read 2 raw sequencing data, aka reverse reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R2\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n FT ICR-MS Analysis Results:\n text: FT ICR-MS Analysis Results\n description: FT ICR-MS-based molecular formula assignment results table\n GC-MS Metabolomics Results:\n text: GC-MS Metabolomics Results\n description: GC-MS-based metabolite assignment results table\n Metaproteomics Workflow Statistics:\n text: Metaproteomics Workflow Statistics\n description: Aggregate workflow statistics file\n Protein Report:\n text: Protein Report\n description: Filtered protein report file\n Peptide Report:\n text: Peptide Report\n description: Filtered peptide report file\n Unfiltered Metaproteomics Results:\n text: Unfiltered Metaproteomics Results\n description: MSGFjobs and MASIC output file\n Read Count and RPKM:\n text: Read Count and RPKM\n description: Annotation read count and RPKM per feature JSON\n QC non-rRNA R2:\n text: QC non-rRNA R2\n description: QC removed rRNA reads (R2) fastq\n QC non-rRNA R1:\n text: QC non-rRNA R1\n description: QC removed rRNA reads (R1) fastq\n Metagenome Bins:\n text: Metagenome Bins\n description: Metagenome bin contigs fasta\n Metagenome Bins Compression File:\n text: Metagenome Bins Compression File\n description: Compressed file containing all metagenome bins and associated files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_hqmq_bin.zip'\n Metagenome Bins Info File:\n text: Metagenome Bins Info File\n description: File containing version information on the binning workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_bin.info'\n CheckM Statistics:\n text: CheckM Statistics\n description: CheckM statistics report\n Read Based Analysis Info File:\n text: Read Based Analysis Info File\n description: File containing reads based analysis information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: profiler.info\n GTDBTK Bacterial Summary:\n text: GTDBTK Bacterial Summary\n description: GTDBTK bacterial summary\n GTDBTK Archaeal Summary:\n text: GTDBTK Archaeal Summary\n description: GTDBTK archaeal summary\n GOTTCHA2 Krona Plot:\n text: GOTTCHA2 Krona Plot\n description: GOTTCHA2 krona plot HTML file\n GOTTCHA2 Classification Report:\n text: GOTTCHA2 Classification Report\n description: GOTTCHA2 classification report file\n GOTTCHA2 Report Full:\n text: GOTTCHA2 Report Full\n description: GOTTCHA2 report file\n Kraken2 Krona Plot:\n text: Kraken2 Krona Plot\n description: Kraken2 krona plot HTML file\n Centrifuge Krona Plot:\n text: Centrifuge Krona Plot\n description: Centrifuge krona plot HTML file\n Centrifuge output report file:\n text: Centrifuge output report file\n description: Centrifuge output report file\n Kraken2 Classification Report:\n text: Kraken2 Classification Report\n description: Kraken2 output report file\n Kraken2 Taxonomic Classification:\n text: Kraken2 Taxonomic Classification\n description: Kraken2 output read classification file\n Centrifuge Classification Report:\n text: Centrifuge Classification Report\n description: Centrifuge output report file\n Centrifuge Taxonomic Classification:\n text: Centrifuge Taxonomic Classification\n description: Centrifuge output read classification file\n Structural Annotation GFF:\n text: Structural Annotation GFF\n description: GFF3 format file with structural annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation.gff'\n Structural Annotation Stats Json:\n text: Structural Annotation Stats Json\n description: Structural annotations stats json\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation_stats.json'\n Functional Annotation GFF:\n text: Functional Annotation GFF\n description: GFF3 format file with functional annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_functional_annotation.gff'\n Annotation Info File:\n text: Annotation Info File\n description: File containing annotation info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_imgap.info'\n Annotation Amino Acid FASTA:\n text: Annotation Amino Acid FASTA\n description: FASTA amino acid file for annotated proteins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_proteins.faa'\n Annotation Enzyme Commission:\n text: Annotation Enzyme Commission\n description: Tab delimited file for EC annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ec.tsv'\n Annotation KEGG Orthology:\n text: Annotation KEGG Orthology\n description: Tab delimited file for KO annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko.tsv'\n Assembly Info File:\n text: Assembly Info File\n description: File containing assembly info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: README.txt\n Assembly Coverage BAM:\n text: Assembly Coverage BAM\n description: Sorted bam file of reads mapping back to the final assembly\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped.sam.gz'\n Assembly AGP:\n text: Assembly AGP\n description: An AGP format file that describes the assembly\n Assembly Scaffolds:\n text: Assembly Scaffolds\n description: Final assembly scaffolds fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_assembly.contigs.fasta'\n Assembly Contigs:\n text: Assembly Contigs\n description: Final assembly contigs fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: assembly.contigs.fasta\n Assembly Coverage Stats:\n text: Assembly Coverage Stats\n description: Assembled contigs coverage information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n Contig Mapping File:\n text: Contig Mapping File\n description: Contig mappings between contigs and scaffolds\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_contig_names_mapping.tsv'\n Error Corrected Reads:\n text: Error Corrected Reads\n description: Error corrected reads fastq\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: input.corr.fastq.gz\n Filtered Sequencing Reads:\n text: Filtered Sequencing Reads\n description: Reads QC result fastq (clean data)\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n Read Filtering Info File:\n text: Read Filtering Info File\n description: File containing read filtering information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_readsQC.info'\n QC Statistics Extended:\n text: QC Statistics Extended\n description: Extended report including methods and results for read filtering\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: /.+?(?=filter)/filtered-report.txt\n QC Statistics:\n text: QC Statistics\n description: Reads QC summary statistics\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_filterStats2.txt'\n TIGRFam Annotation GFF:\n text: TIGRFam Annotation GFF\n description: GFF3 format file with TIGRfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_tigrfam.gff'\n CRT Annotation GFF:\n text: CRT Annotation GFF\n description: GFF3 format file with CRT\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.gff'\n Genemark Annotation GFF:\n text: Genemark Annotation GFF\n description: GFF3 format file with Genemark\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_genemark.gff'\n Prodigal Annotation GFF:\n text: Prodigal Annotation GFF\n description: GFF3 format file with Prodigal\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_prodigal.gff'\n TRNA Annotation GFF:\n text: TRNA Annotation GFF\n description: GFF3 format file with TRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_trna.gff'\n Misc Annotation GFF:\n text: Misc Annotation GFF\n description: GFF3 format file with Misc\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n RFAM Annotation GFF:\n text: RFAM Annotation GFF\n description: GFF3 format file with RFAM\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam.gff'\n TMRNA Annotation GFF:\n text: TMRNA Annotation GFF\n description: GFF3 format file with TMRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n Crispr Terms:\n text: Crispr Terms\n description: Crispr Terms\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.crisprs'\n Product Names:\n text: Product Names\n description: Product names file\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_product_names.tsv'\n Gene Phylogeny tsv:\n text: Gene Phylogeny tsv\n description: Gene Phylogeny tsv\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_gene_phylogeny.tsv'\n Scaffold Lineage tsv:\n text: Scaffold Lineage tsv\n description: phylogeny at the scaffold level\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_scaffold_lineage.tsv'\n Clusters of Orthologous Groups (COG) Annotation GFF:\n text: Clusters of Orthologous Groups (COG) Annotation GFF\n description: GFF3 format file with COGs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cog.gff'\n KO_EC Annotation GFF:\n text: KO_EC Annotation GFF\n description: GFF3 format file with KO_EC\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko_ec.gff'\n CATH FunFams (Functional Families) Annotation GFF:\n text: CATH FunFams (Functional Families) Annotation GFF\n description: GFF3 format file with CATH FunFams\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cath_funfam.gff'\n SUPERFam Annotation GFF:\n text: SUPERFam Annotation GFF\n description: GFF3 format file with SUPERFam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_supfam.gff'\n SMART Annotation GFF:\n text: SMART Annotation GFF\n description: GFF3 format file with SMART\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_smart.gff'\n Pfam Annotation GFF:\n text: Pfam Annotation GFF\n description: GFF3 format file with Pfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pfam.gff'\n Annotation Statistics:\n text: Annotation Statistics\n description: Annotation statistics report\n Direct Infusion FT ICR-MS Raw Data:\n text: Direct Infusion FT ICR-MS Raw Data\n description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n mass spectrometry raw data acquired in broadband full scan mode\n Raw Compressed Metagenome Interleaved Paired-End Reads:\n text: Raw Compressed Metagenome Interleaved Paired-End Reads\n description: Raw sequencing reads from a metagenome that is in interleaved paired-end\n format and compressed using GNU zip format.\n\nURI: FilterTypeEnum
"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":"name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n particulate air filter:\n text: particulate air filter\n chemical air filter:\n text: chemical air filter\n low-MERV pleated media:\n text: low-MERV pleated media\n HEPA:\n text: HEPA\n electrostatic:\n text: electrostatic\n gas-phase or ultraviolet air treatments:\n text: gas-phase or ultraviolet air treatments\n\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: FloorCondEnum
"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":"name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: FloorFinishMatEnum
"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":"name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n tile:\n text: tile\n wood strip or parquet:\n text: wood strip or parquet\n carpet:\n text: carpet\n rug:\n text: rug\n laminate wood:\n text: laminate wood\n lineoleum:\n text: lineoleum\n vinyl composition tile:\n text: vinyl composition tile\n sheet vinyl:\n text: sheet vinyl\n stone:\n text: stone\n bamboo:\n text: bamboo\n cork:\n text: cork\n terrazo:\n text: terrazo\n concrete:\n text: concrete\n none:\n text: none\n sealed:\n text: sealed\n clear finish:\n text: clear finish\n paint:\n text: paint\n none or unfinished:\n text: none or unfinished\n\nURI: FloorStrucEnum
"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":"name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n balcony:\n text: balcony\n floating floor:\n text: floating floor\n glass floor:\n text: glass floor\n raised floor:\n text: raised floor\n sprung floor:\n text: sprung floor\n wood-framed:\n text: wood-framed\n concrete:\n text: concrete\n\nURI: FloorWaterMoldEnum
"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":"name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mold odor:\n text: mold odor\n wet floor:\n text: wet floor\n water stains:\n text: water stains\n wall discoloration:\n text: wall discoloration\n floor discoloration:\n text: floor discoloration\n ceiling discoloration:\n text: ceiling discoloration\n peeling paint or wallpaper:\n text: peeling paint or wallpaper\n bulging walls:\n text: bulging walls\n condensation:\n text: condensation\n\nURI: FreqCleanEnum
"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":"name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Daily:\n text: Daily\n Weekly:\n text: Weekly\n Monthly:\n text: Monthly\n Quarterly:\n text: Quarterly\n Annually:\n text: Annually\n other:\n text: other\n\nAn assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods
URI: nmdc:FunctionalAnnotation
classDiagram\n class FunctionalAnnotation\n FunctionalAnnotation : has_function\n\n FunctionalAnnotation : subject\n\n FunctionalAnnotation --|> GeneProduct : subject\n\n FunctionalAnnotation : was_generated_by\n\n FunctionalAnnotation --|> MetagenomeAnnotationActivity : was_generated_by\n\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows.\n In the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nnotes:\n- move id slot usage patterns to has_function slot usage?\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\nslot_usage:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n domain_of:\n - FunctionalAnnotation\n type:\n name: type\n description: TODO\n range: OntologyClass\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows.\n In the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nnotes:\n- move id slot usage patterns to has_function slot usage?\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n domain_of:\n - FunctionalAnnotation\n type:\n name: type\n description: TODO\n range: OntologyClass\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\nattributes:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_function\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: string\n pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subject\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: GeneProduct\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotation\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\n\nURI: nmdc:FunctionalAnnotationAggMember
classDiagram\n class FunctionalAnnotationAggMember\n FunctionalAnnotationAggMember : count\n\n FunctionalAnnotationAggMember : gene_function_id\n\n FunctionalAnnotationAggMember : metagenome_annotation_id\n\n FunctionalAnnotationAggMember --|> WorkflowExecutionActivity : metagenome_annotation_id\n\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- metagenome_annotation_id\n- gene_function_id\n- count\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n metagenome_annotation_id:\n name: metagenome_annotation_id\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metagenome_annotation_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: WorkflowExecutionActivity\n gene_function_id:\n name: gene_function_id\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_function_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: uriorcurie\n count:\n name: count\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: count\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: integer\n\nAbstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
URI: nmdc:FunctionalAnnotationTerm
classDiagram\n class FunctionalAnnotationTerm\n OntologyClass <|-- FunctionalAnnotationTerm\n\n\n FunctionalAnnotationTerm <|-- Pathway\n FunctionalAnnotationTerm <|-- Reaction\n FunctionalAnnotationTerm <|-- OrthologyGroup\n\n\n FunctionalAnnotationTerm : alternative_identifiers\n\n FunctionalAnnotationTerm : description\n\n FunctionalAnnotationTerm : id\n\n FunctionalAnnotationTerm : name\n\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: FunctionalAnnotationTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FunctionalAnnotationTerm\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FunctionalAnnotationTerm\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: FunctionalAnnotationTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: FurnitureEnum
"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":"name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n chair:\n text: chair\n desks:\n text: desks\n\nURI: GenderRestroomEnum
"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":"name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n all gender:\n text: all gender\n female:\n text: female\n gender neurtral:\n text: gender neurtral\n male:\n text: male\n male and female:\n text: male and female\n unisex:\n text: unisex\n\nA molecule encoded by a gene that has an evolved function
URI: nmdc:GeneProduct
classDiagram\n class GeneProduct\n NamedThing <|-- GeneProduct\n\n GeneProduct : alternative_identifiers\n\n GeneProduct : description\n\n GeneProduct : id\n\n GeneProduct : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
PR
UniProtKB
gtpo
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\n\nname: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: GeneProduct\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: GeneProduct\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: GeneProduct\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: GeneProduct\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nA feature localized to an interval along a genome
URI: nmdc:GenomeFeature
classDiagram\n class GenomeFeature\n GenomeFeature : encodes\n\n GenomeFeature --|> GeneProduct : encodes\n\n GenomeFeature : end\n\n GenomeFeature : feature_type\n\n GenomeFeature : phase\n\n GenomeFeature : seqid\n\n GenomeFeature : start\n\n GenomeFeature : strand\n\n GenomeFeature : type\n\n GenomeFeature --|> OntologyClass : type\n\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\nslot_usage:\n seqid:\n name: seqid\n domain_of:\n - GenomeFeature\n required: true\n type:\n name: type\n description: A type from the sequence ontology\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n start:\n name: start\n domain_of:\n - GenomeFeature\n required: true\n end:\n name: end\n domain_of:\n - GenomeFeature\n required: true\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n seqid:\n name: seqid\n domain_of:\n - GenomeFeature\n required: true\n type:\n name: type\n description: A type from the sequence ontology\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n start:\n name: start\n domain_of:\n - GenomeFeature\n required: true\n end:\n name: end\n domain_of:\n - GenomeFeature\n required: true\nattributes:\n encodes:\n name: encodes\n description: The gene product encoded by this feature. Typically this is used\n for a CDS feature or gene feature which will encode a protein. It can also be\n used by a nc transcript ot gene feature that encoded a ncRNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: encodes\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: GeneProduct\n end:\n name: end\n description: The end of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: gff_coordinate\n alias: end\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n feature_type:\n name: feature_type\n description: 'TODO: Yuri to write'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_type\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n phase:\n name: phase\n description: The phase for a coding sequence entity. For example, phase of a CDS\n as represented in a GFF3 with a value of 0, 1 or 2.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:phase\n rank: 1000\n alias: phase\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n minimum_value: 0\n maximum_value: 2\n seqid:\n name: seqid\n description: The ID of the landmark used to establish the coordinate system for\n the current feature.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: seqid\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n required: true\n start:\n name: start\n description: The start of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: gff_coordinate\n alias: start\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n strand:\n name: strand\n description: The strand on which a feature is located. Has a value of '+' (sense\n strand or forward strand) or '-' (anti-sense strand or reverse strand).\n todos:\n - set the range to an enum?\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:strand\n rank: 1000\n alias: strand\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n type:\n name: type\n description: A type from the sequence ontology\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: GenomeFeature\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n\nA normalized value for a location on the earth's surface
URI: nmdc:GeolocationValue
classDiagram\n class GeolocationValue\n AttributeValue <|-- GeolocationValue\n\n GeolocationValue : has_raw_value\n\n GeolocationValue : latitude\n\n GeolocationValue : longitude\n\n GeolocationValue : was_generated_by\n\n GeolocationValue --|> Activity : was_generated_by\n\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n domain_of:\n - AttributeValue\n - QuantityValue\n latitude:\n name: latitude\n domain_of:\n - GeolocationValue\n required: true\n longitude:\n name: longitude\n domain_of:\n - GeolocationValue\n required: true\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n domain_of:\n - AttributeValue\n - QuantityValue\n latitude:\n name: latitude\n domain_of:\n - GeolocationValue\n required: true\n longitude:\n name: longitude\n domain_of:\n - GeolocationValue\n required: true\nattributes:\n latitude:\n name: latitude\n description: latitude\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: GeolocationValue\n slot_uri: wgs84:lat\n alias: latitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal degree\n required: true\n longitude:\n name: longitude\n description: longitude\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: GeolocationValue\n slot_uri: wgs84:long\n alias: longitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal degree\n required: true\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: GeolocationValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: GeolocationValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: GrowthHabitEnum
"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":"name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n erect:\n text: erect\n semi-erect:\n text: semi-erect\n spreading:\n text: spreading\n prostrate:\n text: prostrate\n\nURI: HandidnessEnum
"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":"name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ambidexterity:\n text: ambidexterity\n left handedness:\n text: left handedness\n mixed-handedness:\n text: mixed-handedness\n right handedness:\n text: right handedness\n\nURI: HcProducedEnum
"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":"name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil:\n text: Oil\n Gas-Condensate:\n text: Gas-Condensate\n Gas:\n text: Gas\n Bitumen:\n text: Bitumen\n Coalbed Methane:\n text: Coalbed Methane\n other:\n text: other\n\nURI: HcrEnum
"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":"name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil Reservoir:\n text: Oil Reservoir\n Gas Reservoir:\n text: Gas Reservoir\n Oil Sand:\n text: Oil Sand\n Coalbed:\n text: Coalbed\n Shale:\n text: Shale\n Tight Oil Reservoir:\n text: Tight Oil Reservoir\n Tight Gas Reservoir:\n text: Tight Gas Reservoir\n other:\n text: other\n\nURI: HcrGeolAgeEnum
"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: HeatCoolTypeEnum
"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":"name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n radiant system:\n text: radiant system\n heat pump:\n text: heat pump\n forced air system:\n text: forced air system\n steam forced heat:\n text: steam forced heat\n wood stove:\n text: wood stove\n\nURI: HeatDelivLocEnum
"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":"name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: HostSexEnum
"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None male None neuter None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":"name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n female:\n text: female\n hermaphrodite:\n text: hermaphrodite\n male:\n text: male\n neuter:\n text: neuter\n\nAn attribute value representing an image.
URI: nmdc:ImageValue
classDiagram\n class ImageValue\n AttributeValue <|-- ImageValue\n\n ImageValue : description\n\n ImageValue : display_order\n\n ImageValue : has_raw_value\n\n ImageValue : url\n\n ImageValue : was_generated_by\n\n ImageValue --|> Activity : was_generated_by\n\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: ImageValue\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ImageValue\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n display_order:\n name: display_order\n description: When rendering information, this attribute to specify the order in\n which the information should be rendered.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: display_order\n owner: ImageValue\n domain_of:\n - ImageValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ImageValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ImageValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: IndoorSpaceEnum
"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":"name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bedroom:\n text: bedroom\n office:\n text: office\n bathroom:\n text: bathroom\n foyer:\n text: foyer\n kitchen:\n text: kitchen\n locker room:\n text: locker room\n hallway:\n text: hallway\n elevator:\n text: elevator\n\nURI: IndoorSurfEnum
"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":"name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n ceiling:\n text: ceiling\n counter top:\n text: counter top\n door:\n text: door\n shelving:\n text: shelving\n vent cover:\n text: vent cover\n window:\n text: window\n wall:\n text: wall\n\nA material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].
URI: nmdc:Instrument
classDiagram\n class Instrument\n NamedThing <|-- Instrument\n\n Instrument : alternative_identifiers\n\n Instrument : description\n\n Instrument : id\n\n Instrument : name\n\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent[OBI].\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000485\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent[OBI].\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000485\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Instrument\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Instrument\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Instrument\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Instrument\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:InstrumentValue
classDiagram\n class InstrumentValue\n AttributeValue <|-- InstrumentValue\n\n InstrumentValue : has_numeric_value\n\n InstrumentValue : has_raw_value\n\n InstrumentValue : has_unit\n\n InstrumentValue : instrument_name\n\n InstrumentValue : was_generated_by\n\n InstrumentValue --|> Activity : was_generated_by\n\n\nname: InstrumentValue\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_unit\n- has_numeric_value\n- instrument_name\n\nname: InstrumentValue\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_unit:\n name: has_unit\n description: Links a QuantityValue to a unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - scale\n mappings:\n - qud:unit\n - schema:unitCode\n rank: 1000\n alias: has_unit\n owner: InstrumentValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n range: unit\n has_numeric_value:\n name: has_numeric_value\n description: Links a quantity value to a number\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: InstrumentValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: float\n instrument_name:\n name: instrument_name\n description: The name of the instrument that was used for processing the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_name\n owner: InstrumentValue\n domain_of:\n - OmicsProcessing\n - InstrumentValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: InstrumentValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: InstrumentValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: IntWallCondEnum
"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":"name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
A value that is an integer
URI: nmdc:IntegerValue
classDiagram\n class IntegerValue\n AttributeValue <|-- IntegerValue\n\n IntegerValue : has_numeric_value\n\n IntegerValue : has_raw_value\n\n IntegerValue : was_generated_by\n\n IntegerValue --|> Activity : was_generated_by\n\n\nname: IntegerValue\ndescription: A value that is an integer\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_numeric_value\n\nname: IntegerValue\ndescription: A value that is an integer\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_numeric_value:\n name: has_numeric_value\n description: Links a quantity value to a number\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: IntegerValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: float\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: IntegerValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: IntegerValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: Investigation
"},{"location":"Investigation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Investigation/#schema-source","title":"Schema Source","text":"URI: JgiContTypeEnum
"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description rna_cont_type Tube or plate (96-well) dna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":"name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plate:\n text: plate\n tube:\n text: tube\n\nA string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: nmdc:LabDevice
classDiagram\n class LabDevice\n LabDevice : activity_speed\n\n LabDevice --|> QuantityValue : activity_speed\n\n LabDevice : activity_temperature\n\n LabDevice --|> QuantityValue : activity_temperature\n\n LabDevice : activity_time\n\n LabDevice --|> QuantityValue : activity_time\n\n LabDevice : device_type\n\n LabDevice --|> DeviceTypeEnum : device_type\n\n\nname: LabDevice\ntitle: Lab device\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- device_type\n- activity_speed\n- activity_temperature\n- activity_time\n\nname: LabDevice\ntitle: Lab device\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n device_type:\n name: device_type\n title: device type\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker type\n rank: 1000\n alias: device_type\n owner: LabDevice\n domain_of:\n - LabDevice\n range: DeviceTypeEnum\n activity_speed:\n name: activity_speed\n title: activity speed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shake_speed\n rank: 1000\n alias: activity_speed\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n activity_temperature:\n name: activity_temperature\n todos:\n - constrain units\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: activity_temperature\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n activity_time:\n name: activity_time\n title: activity time\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shake_time\n rank: 1000\n alias: activity_time\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n\nA language code conforming to ISO_639-1
URI: xsd:language
base: str
uri: xsd:language
URI: nmdc:LibraryPreparation
classDiagram\n class LibraryPreparation\n BiosampleProcessing <|-- LibraryPreparation\n\n LibraryPreparation : alternative_identifiers\n\n LibraryPreparation : description\n\n LibraryPreparation : end_date\n\n LibraryPreparation : has_input\n\n LibraryPreparation --|> Biosample : has_input\n\n LibraryPreparation : has_output\n\n LibraryPreparation --|> NamedThing : has_output\n\n LibraryPreparation : id\n\n LibraryPreparation : library_preparation_kit\n\n LibraryPreparation : library_type\n\n LibraryPreparation --|> LibraryTypeEnum : library_type\n\n LibraryPreparation : name\n\n LibraryPreparation : pcr_cycles\n\n LibraryPreparation : processing_institution\n\n LibraryPreparation --|> processing_institution_enum : processing_institution\n\n LibraryPreparation : protocol_link\n\n LibraryPreparation --|> Protocol : protocol_link\n\n LibraryPreparation : start_date\n\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: BiosampleProcessing\nslots:\n- library_preparation_kit\n- library_type\n- pcr_cycles\n- processing_institution\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n library_preparation_kit:\n name: library_preparation_kit\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_preparation_kit\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: string\n library_type:\n name: library_type\n title: library type\n examples:\n - value: DNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_type\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: LibraryTypeEnum\n pcr_cycles:\n name: pcr_cycles\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - OBI:0002475\n rank: 1000\n alias: pcr_cycles\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: integer\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: LibraryPreparation\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: LibraryPreparation\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: LibraryPreparation\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: LibraryPreparation\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: LibraryPreparation\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: LibraryPreparation\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: LibraryPreparation\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: LibraryPreparation\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: LibraryTypeEnum
"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":"name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n\nURI: LightTypeEnum
"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":"name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n natural light:\n text: natural light\n electric light:\n text: electric light\n desk lamp:\n text: desk lamp\n flourescent lights:\n text: flourescent lights\n none:\n text: none\n\nURI: LithologyEnum
"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":"name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Basement:\n text: Basement\n Chalk:\n text: Chalk\n Chert:\n text: Chert\n Coal:\n text: Coal\n Conglomerate:\n text: Conglomerate\n Diatomite:\n text: Diatomite\n Dolomite:\n text: Dolomite\n Limestone:\n text: Limestone\n Sandstone:\n text: Sandstone\n Shale:\n text: Shale\n Siltstone:\n text: Siltstone\n Volcanic:\n text: Volcanic\n other:\n text: other\n\nURI: nmdc:MagBin
classDiagram\n class MagBin\n MagBin : bin_name\n\n MagBin : bin_quality\n\n MagBin : completeness\n\n MagBin : contamination\n\n MagBin : gene_count\n\n MagBin : gtdbtk_class\n\n MagBin : gtdbtk_domain\n\n MagBin : gtdbtk_family\n\n MagBin : gtdbtk_genus\n\n MagBin : gtdbtk_order\n\n MagBin : gtdbtk_phylum\n\n MagBin : gtdbtk_species\n\n MagBin : members_id\n\n MagBin : num_16s\n\n MagBin : num_23s\n\n MagBin : num_5s\n\n MagBin : num_t_rna\n\n MagBin : number_of_contig\n\n MagBin : total_bases\n\n MagBin : type\n\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n bin_name:\n name: bin_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_name\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n bin_quality:\n name: bin_quality\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_quality\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n completeness:\n name: completeness\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: MagBin\n domain_of:\n - MagBin\n range: float\n contamination:\n name: contamination\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: MagBin\n domain_of:\n - MagBin\n range: float\n gene_count:\n name: gene_count\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_count\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n gtdbtk_class:\n name: gtdbtk_class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_class\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_domain:\n name: gtdbtk_domain\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_domain\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_family:\n name: gtdbtk_family\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_family\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_genus:\n name: gtdbtk_genus\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_genus\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_order:\n name: gtdbtk_order\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_order\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_phylum:\n name: gtdbtk_phylum\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_phylum\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_species:\n name: gtdbtk_species\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_species\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n members_id:\n name: members_id\n todos:\n - this slot needs some basic textual annotations and constraints\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: members_id\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n num_16s:\n name: num_16s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_16s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_23s:\n name: num_23s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_23s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_5s:\n name: num_5s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_5s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_t_rna:\n name: num_t_rna\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_t_rna\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n number_of_contig:\n name: number_of_contig\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: number_of_contig\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n total_bases:\n name: total_bases\n todos:\n - this slot needs some basic textual annotations and constraints\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: total_bases\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MagBin\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n\nA workflow execution activity that uses computational binning tools to group assembled contigs into genomes
URI: nmdc:MagsAnalysisActivity
classDiagram\n class MagsAnalysisActivity\n WorkflowExecutionActivity <|-- MagsAnalysisActivity\n\n MagsAnalysisActivity : binned_contig_num\n\n MagsAnalysisActivity : ended_at_time\n\n MagsAnalysisActivity : execution_resource\n\n MagsAnalysisActivity : git_url\n\n MagsAnalysisActivity : has_input\n\n MagsAnalysisActivity --|> NamedThing : has_input\n\n MagsAnalysisActivity : has_output\n\n MagsAnalysisActivity --|> NamedThing : has_output\n\n MagsAnalysisActivity : id\n\n MagsAnalysisActivity : input_contig_num\n\n MagsAnalysisActivity : low_depth_contig_num\n\n MagsAnalysisActivity : mags_list\n\n MagsAnalysisActivity --|> MagBin : mags_list\n\n MagsAnalysisActivity : name\n\n MagsAnalysisActivity : part_of\n\n MagsAnalysisActivity --|> NamedThing : part_of\n\n MagsAnalysisActivity : started_at_time\n\n MagsAnalysisActivity : too_short_contig_num\n\n MagsAnalysisActivity : type\n\n MagsAnalysisActivity : unbinned_contig_num\n\n MagsAnalysisActivity : used\n\n MagsAnalysisActivity : version\n\n MagsAnalysisActivity : was_informed_by\n\n MagsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MagsAnalysisActivity\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- input_contig_num\n- binned_contig_num\n- too_short_contig_num\n- low_depth_contig_num\n- unbinned_contig_num\n- mags_list\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MagsAnalysisActivity\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MagsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n input_contig_num:\n name: input_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n binned_contig_num:\n name: binned_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: binned_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n too_short_contig_num:\n name: too_short_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: too_short_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n low_depth_contig_num:\n name: low_depth_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: low_depth_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n unbinned_contig_num:\n name: unbinned_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: unbinned_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n mags_list:\n name: mags_list\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: mags_list\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: MagBin\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MagsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MagsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MagsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MagsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MagsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MaterialContainer
classDiagram\n class MaterialContainer\n MaterialContainer : container_size\n\n MaterialContainer --|> QuantityValue : container_size\n\n MaterialContainer : container_type\n\n MaterialContainer --|> ContainerTypeEnum : container_type\n\n\nname: MaterialContainer\ntitle: Material container\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- container_size\n- container_type\n\nname: MaterialContainer\ntitle: Material container\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n container_size:\n name: container_size\n title: container size\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: container_size\n owner: MaterialContainer\n domain_of:\n - MaterialContainer\n range: QuantityValue\n inlined: true\n container_type:\n name: container_type\n title: container type\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: container_type\n owner: MaterialContainer\n domain_of:\n - MaterialContainer\n range: ContainerTypeEnum\n\nURI: nmdc:MaterialEntity
classDiagram\n class MaterialEntity\n NamedThing <|-- MaterialEntity\n\n\n MaterialEntity <|-- Biosample\n MaterialEntity <|-- ProcessedSample\n MaterialEntity <|-- AnalyticalSample\n MaterialEntity <|-- Site\n\n\n MaterialEntity : alternative_identifiers\n\n MaterialEntity : description\n\n MaterialEntity : id\n\n MaterialEntity : name\n\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialEntity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialEntity\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MaterialEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:MaterialSample
classDiagram\n class MaterialSample\n NamedThing <|-- MaterialSample\n\n MaterialSample : alternative_identifiers\n\n MaterialSample : description\n\n MaterialSample : id\n\n MaterialSample : name\n\n\nname: MaterialSample\ntitle: Material sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material entity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MaterialSample\ntitle: Material sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material entity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MaterialSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OBI:0000744
classDiagram\n class MaterialSamplingActivity\n MaterialSamplingActivity : amount_collected\n\n MaterialSamplingActivity --|> QuantityValue : amount_collected\n\n MaterialSamplingActivity : collected_into\n\n MaterialSamplingActivity --|> MaterialContainer : collected_into\n\n MaterialSamplingActivity : material_output\n\n MaterialSamplingActivity --|> MaterialSample : material_output\n\n MaterialSamplingActivity : sampling_method\n\n MaterialSamplingActivity --|> SamplingMethodEnum : sampling_method\n\n\nname: MaterialSamplingActivity\ntitle: Material sampling activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weighing-activity\nslots:\n- amount_collected\n- collected_into\n- material_output\n- sampling_method\nslot_usage:\n amount_collected:\n name: amount_collected\n aliases:\n - weighing-activity.weight\n domain_of:\n - MaterialSamplingActivity\n collected_into:\n name: collected_into\n aliases:\n - weighing-activity.contanier\n domain_of:\n - MaterialSamplingActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:6\n aliases:\n - weighing-activity.id\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nclass_uri: OBI:0000744\n\nname: MaterialSamplingActivity\ntitle: Material sampling activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weighing-activity\nslot_usage:\n amount_collected:\n name: amount_collected\n aliases:\n - weighing-activity.weight\n domain_of:\n - MaterialSamplingActivity\n collected_into:\n name: collected_into\n aliases:\n - weighing-activity.contanier\n domain_of:\n - MaterialSamplingActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:6\n aliases:\n - weighing-activity.id\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nattributes:\n amount_collected:\n name: amount_collected\n title: amount collected\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.weight\n rank: 1000\n alias: amount_collected\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: QuantityValue\n inlined: true\n collected_into:\n name: collected_into\n title: collected into\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.contanier\n rank: 1000\n alias: collected_into\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: MaterialContainer\n inlined: true\n material_output:\n name: material_output\n title: material output\n examples:\n - value: somextract:6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.id\n rank: 1000\n alias: material_output\n owner: MaterialSamplingActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\n sampling_method:\n name: sampling_method\n title: sampling method\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sampling_method\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: SamplingMethodEnum\nclass_uri: OBI:0000744\n\nURI: MechStrucEnum
"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":"name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n subway:\n text: subway\n coach:\n text: coach\n carriage:\n text: carriage\n elevator:\n text: elevator\n escalator:\n text: escalator\n boat:\n text: boat\n train:\n text: train\n car:\n text: car\n bus:\n text: bus\n\nThis is used to link a metabolomics analysis workflow to a specific metabolite
URI: nmdc:MetaboliteQuantification
classDiagram\n class MetaboliteQuantification\n MetaboliteQuantification : alternative_identifiers\n\n MetaboliteQuantification : highest_similarity_score\n\n MetaboliteQuantification : metabolite_quantified\n\n MetaboliteQuantification --|> ChemicalEntity : metabolite_quantified\n\n\nname: MetaboliteQuantification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_quantified\n\nname: MetaboliteQuantification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MetaboliteQuantification\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n highest_similarity_score:\n name: highest_similarity_score\n todos:\n - Yuri to fill in description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: highest_similarity_score\n owner: MetaboliteQuantification\n domain_of:\n - MetaboliteQuantification\n range: float\n metabolite_quantified:\n name: metabolite_quantified\n description: the specific metabolite identifier\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metabolite_quantified\n owner: MetaboliteQuantification\n domain_of:\n - MetaboliteQuantification\n range: ChemicalEntity\n\nURI: nmdc:MetabolomicsAnalysisActivity
classDiagram\n class MetabolomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetabolomicsAnalysisActivity\n\n MetabolomicsAnalysisActivity : ended_at_time\n\n MetabolomicsAnalysisActivity : execution_resource\n\n MetabolomicsAnalysisActivity : git_url\n\n MetabolomicsAnalysisActivity : has_calibration\n\n MetabolomicsAnalysisActivity : has_input\n\n MetabolomicsAnalysisActivity --|> NamedThing : has_input\n\n MetabolomicsAnalysisActivity : has_metabolite_quantifications\n\n MetabolomicsAnalysisActivity --|> MetaboliteQuantification : has_metabolite_quantifications\n\n MetabolomicsAnalysisActivity : has_output\n\n MetabolomicsAnalysisActivity --|> NamedThing : has_output\n\n MetabolomicsAnalysisActivity : id\n\n MetabolomicsAnalysisActivity : name\n\n MetabolomicsAnalysisActivity : part_of\n\n MetabolomicsAnalysisActivity --|> NamedThing : part_of\n\n MetabolomicsAnalysisActivity : started_at_time\n\n MetabolomicsAnalysisActivity : type\n\n MetabolomicsAnalysisActivity : used\n\n MetabolomicsAnalysisActivity : version\n\n MetabolomicsAnalysisActivity : was_informed_by\n\n MetabolomicsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MetabolomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_calibration\n- has_metabolite_quantifications\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetabolomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_calibration:\n name: has_calibration\n description: A reference to a file that holds calibration information.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_calibration\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n - NomAnalysisActivity\n range: string\n has_metabolite_quantifications:\n name: has_metabolite_quantifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_metabolite_quantifications\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n range: MetaboliteQuantification\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nThis documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).
Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).
All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.
Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/
"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.
To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC schema includes environmental descriptors from the GSC MIxS standards.
Explore how to create a MIxS-compliant sample metadata spreadsheet
Review our example spreadsheet with sample metadata that has been converted to be compliant with the MIxS Soil environment package. Note that not all non-mandatory terms from the MIxs Soil package were relevant for these example samples, and hence were omitted for clarity.
Basic sample spreadsheet (Tab 1 - before conversion to MIxS)
MIxS-compliant soil spreadsheet (Tab 2 - converted to MIxS Soil)
Explore the mandatory, unique, and shared descriptors from the MIxS Soil package
Searchable descriptors from all MIxS environmental packages - coming soon!
Learn more about all of the 17 MIxS environmental packages
The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.
Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).
Overview of the GOLD ecosystem paths
Ecosystem describes biosamples using three different broadest contexts, namely environmental, engineered, and host-associated.
Ecosystem category subdivides the ecosystem into categories, such as aquatic or terrestrial.
Ecosystem type classifies those categories into types, such as freshwater or marine, cave, desert, soil, etc.
Ecosystem subtype allows for additional environmental context or boundaries.
Specific ecosystem that describes the environment that directly influences the sample or the environmental material itself.
Explore how to map sample environments using the GOLD ecosystem classification
Learn more about the GOLD ecosystem paths using an interactive visualization tool.
Review a step-by-step example of how to assign the GOLD ecosystem classification to a lake sediment sample.
The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.
EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.
MIxS: env_broad_scale (a.k.a. Biome): The major environmental system that the sample or specimen came from. Often, the value for this term comes from EnvO\u2019s biome hierarchy, and is similar to GOLD\u2019s Ecosystem category.
MIxS: env_local_scale (a.k.a. Feature): A more direct expression of the sample or specimen\u2019s local vicinity, which likely has a significant influence on the sample or specimen. Possible values are listed in EnvO\u2019s astronomical body part hierarchy, which is similar to GOLD\u2019s Ecosystem type/subtype.
MIxS: env_medium (a.k.a. material): The environmental material(s) immediately surrounding your sample or specimen prior to sampling. Examples of this are found in EnvO\u2019s environmental material hierarchy, and is similar to GOLD\u2019s Specific ecosystem.
Explore how to map sample environments using the EnvO ecosystem classification
Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.
env_broad_scale (Biome)
Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.
env_local_scale (Feature)
Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.
env_medium (Material)
Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.
Therefore, the EnvO triad for oligotrophic lake sediment is:
Env_broad_scale: freshwater lake biome [ENVO_01000252]
Env_local_scale: oligotrophic lake [ENVO_01000774]
Env_medium: lake sediment [ENVO_00000546]
"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.
Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.
"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.
"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC schema can be found here.
For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.
"},{"location":"MetagenomeAnnotationActivity/","title":"Class: MetagenomeAnnotationActivity","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
URI: nmdc:MetagenomeAnnotationActivity
classDiagram\n class MetagenomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetagenomeAnnotationActivity\n\n MetagenomeAnnotationActivity : ended_at_time\n\n MetagenomeAnnotationActivity : execution_resource\n\n MetagenomeAnnotationActivity : git_url\n\n MetagenomeAnnotationActivity : gold_analysis_project_identifiers\n\n MetagenomeAnnotationActivity : has_input\n\n MetagenomeAnnotationActivity --|> NamedThing : has_input\n\n MetagenomeAnnotationActivity : has_output\n\n MetagenomeAnnotationActivity --|> NamedThing : has_output\n\n MetagenomeAnnotationActivity : id\n\n MetagenomeAnnotationActivity : name\n\n MetagenomeAnnotationActivity : part_of\n\n MetagenomeAnnotationActivity --|> NamedThing : part_of\n\n MetagenomeAnnotationActivity : started_at_time\n\n MetagenomeAnnotationActivity : type\n\n MetagenomeAnnotationActivity : used\n\n MetagenomeAnnotationActivity : version\n\n MetagenomeAnnotationActivity : was_informed_by\n\n MetagenomeAnnotationActivity --|> Activity : was_informed_by\n\n\nname: MetagenomeAnnotationActivity\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeAnnotationActivity\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeAnnotationActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_analysis_project_identifiers\n owner: MetagenomeAnnotationActivity\n domain_of:\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n range: external_identifier\n pattern: ^gold:Ga[0-9]+$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeAnnotationActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeAnnotationActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeAnnotationActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n\nA workflow execution activity that converts sequencing reads into an assembled metagenome.
URI: nmdc:MetagenomeAssembly
classDiagram\n class MetagenomeAssembly\n WorkflowExecutionActivity <|-- MetagenomeAssembly\n\n MetagenomeAssembly : asm_score\n\n MetagenomeAssembly : contig_bp\n\n MetagenomeAssembly : contigs\n\n MetagenomeAssembly : ctg_l50\n\n MetagenomeAssembly : ctg_l90\n\n MetagenomeAssembly : ctg_logsum\n\n MetagenomeAssembly : ctg_max\n\n MetagenomeAssembly : ctg_n50\n\n MetagenomeAssembly : ctg_n90\n\n MetagenomeAssembly : ctg_powsum\n\n MetagenomeAssembly : ended_at_time\n\n MetagenomeAssembly : execution_resource\n\n MetagenomeAssembly : gap_pct\n\n MetagenomeAssembly : gc_avg\n\n MetagenomeAssembly : gc_std\n\n MetagenomeAssembly : git_url\n\n MetagenomeAssembly : has_input\n\n MetagenomeAssembly --|> NamedThing : has_input\n\n MetagenomeAssembly : has_output\n\n MetagenomeAssembly --|> NamedThing : has_output\n\n MetagenomeAssembly : id\n\n MetagenomeAssembly : insdc_assembly_identifiers\n\n MetagenomeAssembly : name\n\n MetagenomeAssembly : num_aligned_reads\n\n MetagenomeAssembly : num_input_reads\n\n MetagenomeAssembly : part_of\n\n MetagenomeAssembly --|> NamedThing : part_of\n\n MetagenomeAssembly : scaf_bp\n\n MetagenomeAssembly : scaf_l50\n\n MetagenomeAssembly : scaf_l90\n\n MetagenomeAssembly : scaf_l_gt50k\n\n MetagenomeAssembly : scaf_logsum\n\n MetagenomeAssembly : scaf_max\n\n MetagenomeAssembly : scaf_n50\n\n MetagenomeAssembly : scaf_n90\n\n MetagenomeAssembly : scaf_n_gt50k\n\n MetagenomeAssembly : scaf_pct_gt50k\n\n MetagenomeAssembly : scaf_powsum\n\n MetagenomeAssembly : scaffolds\n\n MetagenomeAssembly : started_at_time\n\n MetagenomeAssembly : type\n\n MetagenomeAssembly : used\n\n MetagenomeAssembly : version\n\n MetagenomeAssembly : was_informed_by\n\n MetagenomeAssembly --|> Activity : was_informed_by\n\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeAssembly\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeAssembly\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeAssembly\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeAssembly\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAssembly\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAssembly\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n\nInitial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
URI: nmdc:MetagenomeSequencingActivity
classDiagram\n class MetagenomeSequencingActivity\n WorkflowExecutionActivity <|-- MetagenomeSequencingActivity\n\n MetagenomeSequencingActivity : ended_at_time\n\n MetagenomeSequencingActivity : execution_resource\n\n MetagenomeSequencingActivity : git_url\n\n MetagenomeSequencingActivity : has_input\n\n MetagenomeSequencingActivity --|> NamedThing : has_input\n\n MetagenomeSequencingActivity : has_output\n\n MetagenomeSequencingActivity --|> NamedThing : has_output\n\n MetagenomeSequencingActivity : id\n\n MetagenomeSequencingActivity : name\n\n MetagenomeSequencingActivity : part_of\n\n MetagenomeSequencingActivity --|> NamedThing : part_of\n\n MetagenomeSequencingActivity : started_at_time\n\n MetagenomeSequencingActivity : type\n\n MetagenomeSequencingActivity : used\n\n MetagenomeSequencingActivity : version\n\n MetagenomeSequencingActivity : was_informed_by\n\n MetagenomeSequencingActivity --|> Activity : was_informed_by\n\n\nname: MetagenomeSequencingActivity\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeSequencingActivity\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeSequencingActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeSequencingActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeSequencingActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeSequencingActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeSequencingActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeSequencingActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetaproteomicsAnalysisActivity
classDiagram\n class MetaproteomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetaproteomicsAnalysisActivity\n\n MetaproteomicsAnalysisActivity : ended_at_time\n\n MetaproteomicsAnalysisActivity : execution_resource\n\n MetaproteomicsAnalysisActivity : git_url\n\n MetaproteomicsAnalysisActivity : has_input\n\n MetaproteomicsAnalysisActivity --|> NamedThing : has_input\n\n MetaproteomicsAnalysisActivity : has_output\n\n MetaproteomicsAnalysisActivity --|> NamedThing : has_output\n\n MetaproteomicsAnalysisActivity : has_peptide_quantifications\n\n MetaproteomicsAnalysisActivity --|> PeptideQuantification : has_peptide_quantifications\n\n MetaproteomicsAnalysisActivity : id\n\n MetaproteomicsAnalysisActivity : name\n\n MetaproteomicsAnalysisActivity : part_of\n\n MetaproteomicsAnalysisActivity --|> NamedThing : part_of\n\n MetaproteomicsAnalysisActivity : started_at_time\n\n MetaproteomicsAnalysisActivity : type\n\n MetaproteomicsAnalysisActivity : used\n\n MetaproteomicsAnalysisActivity : version\n\n MetaproteomicsAnalysisActivity : was_informed_by\n\n MetaproteomicsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MetaproteomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_peptide_quantifications\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetaproteomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_peptide_quantifications:\n name: has_peptide_quantifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_peptide_quantifications\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - MetaproteomicsAnalysisActivity\n range: PeptideQuantification\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Activity\n alias: used\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nA metatranscriptome activity that e.g. pools assembly and annotation activity.
URI: nmdc:MetatranscriptomeActivity
classDiagram\n class MetatranscriptomeActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeActivity\n\n MetatranscriptomeActivity : ended_at_time\n\n MetatranscriptomeActivity : execution_resource\n\n MetatranscriptomeActivity : git_url\n\n MetatranscriptomeActivity : has_input\n\n MetatranscriptomeActivity --|> NamedThing : has_input\n\n MetatranscriptomeActivity : has_output\n\n MetatranscriptomeActivity --|> NamedThing : has_output\n\n MetatranscriptomeActivity : id\n\n MetatranscriptomeActivity : name\n\n MetatranscriptomeActivity : part_of\n\n MetatranscriptomeActivity --|> NamedThing : part_of\n\n MetatranscriptomeActivity : started_at_time\n\n MetatranscriptomeActivity : type\n\n MetatranscriptomeActivity : used\n\n MetatranscriptomeActivity : version\n\n MetatranscriptomeActivity : was_informed_by\n\n MetatranscriptomeActivity --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeActivity\ndescription: A metatranscriptome activity that e.g. pools assembly and annotation\n activity.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeActivity\ndescription: A metatranscriptome activity that e.g. pools assembly and annotation\n activity.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetatranscriptomeAnnotationActivity
classDiagram\n class MetatranscriptomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeAnnotationActivity\n\n MetatranscriptomeAnnotationActivity : ended_at_time\n\n MetatranscriptomeAnnotationActivity : execution_resource\n\n MetatranscriptomeAnnotationActivity : git_url\n\n MetatranscriptomeAnnotationActivity : gold_analysis_project_identifiers\n\n MetatranscriptomeAnnotationActivity : has_input\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : has_input\n\n MetatranscriptomeAnnotationActivity : has_output\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : has_output\n\n MetatranscriptomeAnnotationActivity : id\n\n MetatranscriptomeAnnotationActivity : name\n\n MetatranscriptomeAnnotationActivity : part_of\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : part_of\n\n MetatranscriptomeAnnotationActivity : started_at_time\n\n MetatranscriptomeAnnotationActivity : type\n\n MetatranscriptomeAnnotationActivity : used\n\n MetatranscriptomeAnnotationActivity : version\n\n MetatranscriptomeAnnotationActivity : was_informed_by\n\n MetatranscriptomeAnnotationActivity --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeAnnotationActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeAnnotationActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_analysis_project_identifiers\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n range: external_identifier\n pattern: ^gold:Ga[0-9]+$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetatranscriptomeAssembly
classDiagram\n class MetatranscriptomeAssembly\n WorkflowExecutionActivity <|-- MetatranscriptomeAssembly\n\n MetatranscriptomeAssembly : asm_score\n\n MetatranscriptomeAssembly : contig_bp\n\n MetatranscriptomeAssembly : contigs\n\n MetatranscriptomeAssembly : ctg_l50\n\n MetatranscriptomeAssembly : ctg_l90\n\n MetatranscriptomeAssembly : ctg_logsum\n\n MetatranscriptomeAssembly : ctg_max\n\n MetatranscriptomeAssembly : ctg_n50\n\n MetatranscriptomeAssembly : ctg_n90\n\n MetatranscriptomeAssembly : ctg_powsum\n\n MetatranscriptomeAssembly : ended_at_time\n\n MetatranscriptomeAssembly : execution_resource\n\n MetatranscriptomeAssembly : gap_pct\n\n MetatranscriptomeAssembly : gc_avg\n\n MetatranscriptomeAssembly : gc_std\n\n MetatranscriptomeAssembly : git_url\n\n MetatranscriptomeAssembly : has_input\n\n MetatranscriptomeAssembly --|> NamedThing : has_input\n\n MetatranscriptomeAssembly : has_output\n\n MetatranscriptomeAssembly --|> NamedThing : has_output\n\n MetatranscriptomeAssembly : id\n\n MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n MetatranscriptomeAssembly : name\n\n MetatranscriptomeAssembly : num_aligned_reads\n\n MetatranscriptomeAssembly : num_input_reads\n\n MetatranscriptomeAssembly : part_of\n\n MetatranscriptomeAssembly --|> NamedThing : part_of\n\n MetatranscriptomeAssembly : scaf_bp\n\n MetatranscriptomeAssembly : scaf_l50\n\n MetatranscriptomeAssembly : scaf_l90\n\n MetatranscriptomeAssembly : scaf_l_gt50k\n\n MetatranscriptomeAssembly : scaf_logsum\n\n MetatranscriptomeAssembly : scaf_max\n\n MetatranscriptomeAssembly : scaf_n50\n\n MetatranscriptomeAssembly : scaf_n90\n\n MetatranscriptomeAssembly : scaf_n_gt50k\n\n MetatranscriptomeAssembly : scaf_pct_gt50k\n\n MetatranscriptomeAssembly : scaf_powsum\n\n MetatranscriptomeAssembly : scaffolds\n\n MetatranscriptomeAssembly : started_at_time\n\n MetatranscriptomeAssembly : type\n\n MetatranscriptomeAssembly : used\n\n MetatranscriptomeAssembly : version\n\n MetatranscriptomeAssembly : was_informed_by\n\n MetatranscriptomeAssembly --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeAssembly\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeAssembly\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeAssembly\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeAssembly\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAssembly\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAssembly\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n\nURI: MixsEnvironmentalTriad
"},{"location":"MixsEnvironmentalTriad/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsEnvironmentalTriad/#schema-source","title":"Schema Source","text":"URI: MixsExtension
"},{"location":"MixsExtension/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsExtension/#schema-source","title":"Schema Source","text":"Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:
URI: https://w3id.org/nmdc/nmdc
"},{"location":"NamedThing/","title":"Class: NamedThing","text":"a databased entity or concept/class
URI: nmdc:NamedThing
classDiagram\n class NamedThing\n NamedThing <|-- DataObject\n NamedThing <|-- Study\n NamedThing <|-- MaterialEntity\n NamedThing <|-- PlannedProcess\n NamedThing <|-- OntologyClass\n NamedThing <|-- Instrument\n NamedThing <|-- GeneProduct\n NamedThing <|-- MaterialSample\n\n NamedThing : alternative_identifiers\n\n NamedThing : description\n\n NamedThing : id\n\n NamedThing : name\n\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: NamedThing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NamedThing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NamedThing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: NamedThing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
A URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: nmdc:NomAnalysisActivity
classDiagram\n class NomAnalysisActivity\n WorkflowExecutionActivity <|-- NomAnalysisActivity\n\n NomAnalysisActivity : ended_at_time\n\n NomAnalysisActivity : execution_resource\n\n NomAnalysisActivity : git_url\n\n NomAnalysisActivity : has_calibration\n\n NomAnalysisActivity : has_input\n\n NomAnalysisActivity --|> NamedThing : has_input\n\n NomAnalysisActivity : has_output\n\n NomAnalysisActivity --|> NamedThing : has_output\n\n NomAnalysisActivity : id\n\n NomAnalysisActivity : name\n\n NomAnalysisActivity : part_of\n\n NomAnalysisActivity --|> NamedThing : part_of\n\n NomAnalysisActivity : started_at_time\n\n NomAnalysisActivity : type\n\n NomAnalysisActivity : used\n\n NomAnalysisActivity : version\n\n NomAnalysisActivity : was_informed_by\n\n NomAnalysisActivity --|> Activity : was_informed_by\n\n\nname: NomAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_calibration\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n range: string\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: NomAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n range: string\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_calibration:\n name: has_calibration\n description: A reference to a file that holds calibration information.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_calibration\n owner: NomAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n - NomAnalysisActivity\n range: string\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: NomAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: NomAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: NomAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: NomAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: NomAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NomAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Activity\n alias: used\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: NucleicAcidSequenceSource
"},{"location":"NucleicAcidSequenceSource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleicAcidSequenceSource/#schema-source","title":"Schema Source","text":"A URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
URI: OccupDocumentEnum
"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":"name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n automated count:\n text: automated count\n estimate:\n text: estimate\n manual count:\n text: manual count\n videos:\n text: videos\n\nThe methods and processes used to generate omics data from a biosample or organism.
URI: nmdc:OmicsProcessing
classDiagram\n class OmicsProcessing\n PlannedProcess <|-- OmicsProcessing\n\n OmicsProcessing : add_date\n\n OmicsProcessing : alternative_identifiers\n\n OmicsProcessing : chimera_check\n\n OmicsProcessing --|> TextValue : chimera_check\n\n OmicsProcessing : description\n\n OmicsProcessing : end_date\n\n OmicsProcessing : gold_sequencing_project_identifiers\n\n OmicsProcessing : has_input\n\n OmicsProcessing --|> NamedThing : has_input\n\n OmicsProcessing : has_output\n\n OmicsProcessing --|> NamedThing : has_output\n\n OmicsProcessing : id\n\n OmicsProcessing : insdc_experiment_identifiers\n\n OmicsProcessing : instrument_name\n\n OmicsProcessing : mod_date\n\n OmicsProcessing : name\n\n OmicsProcessing : ncbi_project_name\n\n OmicsProcessing : nucl_acid_amp\n\n OmicsProcessing --|> TextValue : nucl_acid_amp\n\n OmicsProcessing : nucl_acid_ext\n\n OmicsProcessing --|> TextValue : nucl_acid_ext\n\n OmicsProcessing : omics_type\n\n OmicsProcessing --|> ControlledTermValue : omics_type\n\n OmicsProcessing : part_of\n\n OmicsProcessing --|> NamedThing : part_of\n\n OmicsProcessing : pcr_cond\n\n OmicsProcessing --|> TextValue : pcr_cond\n\n OmicsProcessing : pcr_primers\n\n OmicsProcessing --|> TextValue : pcr_primers\n\n OmicsProcessing : principal_investigator\n\n OmicsProcessing --|> PersonValue : principal_investigator\n\n OmicsProcessing : processing_institution\n\n OmicsProcessing --|> processing_institution_enum : processing_institution\n\n OmicsProcessing : protocol_link\n\n OmicsProcessing --|> Protocol : protocol_link\n\n OmicsProcessing : samp_vol_we_dna_ext\n\n OmicsProcessing --|> QuantityValue : samp_vol_we_dna_ext\n\n OmicsProcessing : seq_meth\n\n OmicsProcessing --|> TextValue : seq_meth\n\n OmicsProcessing : seq_quality_check\n\n OmicsProcessing --|> TextValue : seq_quality_check\n\n OmicsProcessing : start_date\n\n OmicsProcessing : target_gene\n\n OmicsProcessing --|> TextValue : target_gene\n\n OmicsProcessing : target_subfragment\n\n OmicsProcessing --|> TextValue : target_subfragment\n\n OmicsProcessing : type\n\n\nname: OmicsProcessing\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\ncomments:\n- The ID prefix for objects coming from GOLD will be gold:Gp\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nslots:\n- add_date\n- chimera_check\n- gold_sequencing_project_identifiers\n- has_input\n- has_output\n- insdc_experiment_identifiers\n- instrument_name\n- mod_date\n- ncbi_project_name\n- nucl_acid_amp\n- nucl_acid_ext\n- omics_type\n- part_of\n- pcr_cond\n- pcr_primers\n- principal_investigator\n- processing_institution\n- samp_vol_we_dna_ext\n- seq_meth\n- seq_quality_check\n- target_gene\n- target_subfragment\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n\nname: OmicsProcessing\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\ncomments:\n- The ID prefix for objects coming from GOLD will be gold:Gp\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\nattributes:\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n chimera_check:\n name: chimera_check\n annotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\n description: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised\n of two or more phylogenetically distinct parent sequences.\n title: chimera check software\n examples:\n - value: uchime;v4.1;default parameters\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chimera check software\n rank: 1000\n is_a: sequencing field\n string_serialization: '{software};{version};{parameters}'\n slot_uri: MIXS:0000052\n multivalued: false\n alias: chimera_check\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n gold_sequencing_project_identifiers:\n name: gold_sequencing_project_identifiers\n description: identifiers for corresponding sequencing project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Gp0108335\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: omics_processing_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_sequencing_project_identifiers\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: external_identifier\n pattern: ^gold:Gp[0-9]+$\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: OmicsProcessing\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n multivalued: true\n alias: insdc_experiment_identifiers\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: external_identifier\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n instrument_name:\n name: instrument_name\n description: The name of the instrument that was used for processing the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_name\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n - InstrumentValue\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n ncbi_project_name:\n name: ncbi_project_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_project_name\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: string\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n multivalued: false\n alias: nucl_acid_amp\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucl_acid_ext:\n name: nucl_acid_ext\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the material separation to recover\n the nucleic acid fraction from a sample\n title: nucleic acid extraction\n examples:\n - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid extraction\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000037\n multivalued: false\n alias: nucl_acid_ext\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n omics_type:\n name: omics_type\n description: The type of omics data\n notes:\n - was the range string at one point? the values in MongoDB don't look like NMDC\n classes\n examples:\n - value: metatranscriptome\n - value: metagenome\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: omics_type\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: ControlledTermValue\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: OmicsProcessing\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n multivalued: false\n alias: pcr_cond\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n multivalued: false\n alias: pcr_primers\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n is_a: attribute\n alias: principal_investigator\n owner: OmicsProcessing\n domain_of:\n - Study\n - OmicsProcessing\n range: PersonValue\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: OmicsProcessing\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n samp_vol_we_dna_ext:\n name: samp_vol_we_dna_ext\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\n description: 'Volume (ml) or mass (g) of total collected sample processed for\n DNA extraction. Note: total sample collected should be entered under the term\n Sample Size (MIXS:0000001).'\n title: sample volume or weight for DNA extraction\n examples:\n - value: 1500 milliliter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample volume or weight for DNA extraction\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000111\n multivalued: false\n alias: samp_vol_we_dna_ext\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: QuantityValue\n seq_meth:\n name: seq_meth\n annotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\n description: Sequencing machine used. Where possible the term should be taken\n from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\n title: sequencing method\n examples:\n - value: 454 Genome Sequencer FLX [OBI:0000702]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequencing method\n rank: 1000\n is_a: sequencing field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000050\n multivalued: false\n alias: seq_meth\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n seq_quality_check:\n name: seq_quality_check\n annotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\n description: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or\n chromatograms). Applied only for sequences that are not submitted to SRA,ENA\n or DRA\n title: sequence quality check\n examples:\n - value: none\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequence quality check\n rank: 1000\n is_a: sequencing field\n string_serialization: '[none|manually edited]'\n slot_uri: MIXS:0000051\n multivalued: false\n alias: seq_quality_check\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n multivalued: false\n alias: target_gene\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n multivalued: false\n alias: target_subfragment\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: OmicsProcessing\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: OmicsProcessing\n domain_of:\n - PlannedProcess\n range: string\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: OmicsProcessing\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: OmicsProcessing\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OmicsProcessing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OmicsProcessing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:OntologyClass
classDiagram\n class OntologyClass\n NamedThing <|-- OntologyClass\n\n\n OntologyClass <|-- EnvironmentalMaterialTerm\n OntologyClass <|-- ChemicalEntity\n OntologyClass <|-- FunctionalAnnotationTerm\n\n\n OntologyClass : alternative_identifiers\n\n OntologyClass : description\n\n OntologyClass : id\n\n OntologyClass : name\n\n\nname: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nname: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OntologyClass\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OntologyClass\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OntologyClass\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OntologyClass\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OrganismCountEnum
"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":"name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ATP:\n text: ATP\n MPN:\n text: MPN\n other:\n text: other\n\nA set of genes or gene products in which all members are orthologous
URI: nmdc:OrthologyGroup
classDiagram\n class OrthologyGroup\n FunctionalAnnotationTerm <|-- OrthologyGroup\n\n OrthologyGroup : alternative_identifiers\n\n OrthologyGroup : description\n\n OrthologyGroup : id\n\n OrthologyGroup : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CATH
EGGNOG
KEGG.ORTHOLOGY
PANTHER.FAMILY
PFAM
SUPFAM
TIGRFAM
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\n\nname: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OrthologyGroup\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OrthologyGroup\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OrthologyGroup\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OrthologyGroup\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OxyStatSampEnum
"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample oxy_stat_samp"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":"name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aerobic:\n text: aerobic\n anaerobic:\n text: anaerobic\n other:\n text: other\n\nA MIxS package. These can be combined with checklists
URI: Package
"},{"location":"Package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Package/#schema-source","title":"Schema Source","text":"A pathway is a sequence of steps/reactions carried out by an organism or community of organisms
URI: nmdc:Pathway
classDiagram\n class Pathway\n FunctionalAnnotationTerm <|-- Pathway\n\n Pathway : alternative_identifiers\n\n Pathway : description\n\n Pathway : has_part\n\n Pathway --|> Reaction : has_part\n\n Pathway : id\n\n Pathway : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG_PATHWAY
COG
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nslots:\n- has_part\n\nname: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n has_part:\n name: has_part\n description: A pathway can be broken down to a series of reaction step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_part\n owner: Pathway\n domain_of:\n - Pathway\n range: Reaction\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Pathway\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pathway\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pathway\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Pathway\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information
URI: nmdc:PeptideQuantification
classDiagram\n class PeptideQuantification\n PeptideQuantification : all_proteins\n\n PeptideQuantification --|> GeneProduct : all_proteins\n\n PeptideQuantification : best_protein\n\n PeptideQuantification --|> GeneProduct : best_protein\n\n PeptideQuantification : min_q_value\n\n PeptideQuantification : peptide_sequence\n\n PeptideQuantification : peptide_spectral_count\n\n PeptideQuantification : peptide_sum_masic_abundance\n\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: all_proteins\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n min_q_value:\n name: min_q_value\n description: smallest Q-Value associated with the peptide sequence as provided\n by MSGFPlus tool\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - OBI:0001442\n rank: 1000\n alias: min_q_value\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: float\n peptide_sequence:\n name: peptide_sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: string\n peptide_spectral_count:\n name: peptide_spectral_count\n description: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_spectral_count\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n peptide_sum_masic_abundance:\n name: peptide_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the peptide sequence from a given LC-MS/MS data file using the\n MASIC tool\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sum_masic_abundance\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n\nAn attribute value representing a person
URI: nmdc:PersonValue
classDiagram\n class PersonValue\n AttributeValue <|-- PersonValue\n\n PersonValue : email\n\n PersonValue : has_raw_value\n\n PersonValue : name\n\n PersonValue : orcid\n\n PersonValue : profile_image_url\n\n PersonValue : was_generated_by\n\n PersonValue --|> Activity : was_generated_by\n\n PersonValue : websites\n\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n domain_of:\n - PersonValue\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n domain_of:\n - PersonValue\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n domain_of:\n - AttributeValue\n - QuantityValue\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n domain_of:\n - PersonValue\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n domain_of:\n - PersonValue\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n domain_of:\n - AttributeValue\n - QuantityValue\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\nattributes:\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n description: An email address for an entity such as a person. This should be the\n primary email address used.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: schema:email\n alias: email\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PersonValue\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n description: The ORCID of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: PersonValue\n alias: orcid\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n profile_image_url:\n name: profile_image_url\n description: A url that points to an image of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: PersonValue\n alias: profile_image_url\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n websites:\n name: websites\n description: A list of websites that are associated with the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: websites\n owner: PersonValue\n domain_of:\n - Study\n - PersonValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: PersonValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: PersonValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: OBI:0000011
classDiagram\n class PlannedProcess\n NamedThing <|-- PlannedProcess\n\n\n PlannedProcess <|-- CollectingBiosamplesFromSite\n PlannedProcess <|-- BiosampleProcessing\n PlannedProcess <|-- OmicsProcessing\n\n\n PlannedProcess : alternative_identifiers\n\n PlannedProcess : description\n\n PlannedProcess : end_date\n\n PlannedProcess : has_input\n\n PlannedProcess --|> NamedThing : has_input\n\n PlannedProcess : has_output\n\n PlannedProcess --|> NamedThing : has_output\n\n PlannedProcess : id\n\n PlannedProcess : name\n\n PlannedProcess : protocol_link\n\n PlannedProcess --|> Protocol : protocol_link\n\n PlannedProcess : start_date\n\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- end_date\n- has_input\n- has_output\n- protocol_link\n- start_date\nclass_uri: OBI:0000011\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: PlannedProcess\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: PlannedProcess\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: PlannedProcess\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: PlannedProcess\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PlannedProcess\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: PlannedProcess\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: PlannedProcess\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nclass_uri: OBI:0000011\n\nURI: PlantGrowthMedEnum
"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":"name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n other artificial liquid medium:\n text: other artificial liquid medium\n other artificial solid medium:\n text: other artificial solid medium\n peat moss:\n text: peat moss\n perlite:\n text: perlite\n pumice:\n text: pumice\n sand:\n text: sand\n soil:\n text: soil\n vermiculite:\n text: vermiculite\n water:\n text: water\n\nURI: PlantSexEnum
"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":"name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Androdioecious:\n text: Androdioecious\n Androecious:\n text: Androecious\n Androgynous:\n text: Androgynous\n Androgynomonoecious:\n text: Androgynomonoecious\n Andromonoecious:\n text: Andromonoecious\n Bisexual:\n text: Bisexual\n Dichogamous:\n text: Dichogamous\n Diclinous:\n text: Diclinous\n Dioecious:\n text: Dioecious\n Gynodioecious:\n text: Gynodioecious\n Gynoecious:\n text: Gynoecious\n Gynomonoecious:\n text: Gynomonoecious\n Hermaphroditic:\n text: Hermaphroditic\n Imperfect:\n text: Imperfect\n Monoclinous:\n text: Monoclinous\n Monoecious:\n text: Monoecious\n Perfect:\n text: Perfect\n Polygamodioecious:\n text: Polygamodioecious\n Polygamomonoecious:\n text: Polygamomonoecious\n Polygamous:\n text: Polygamous\n Protandrous:\n text: Protandrous\n Protogynous:\n text: Protogynous\n Subandroecious:\n text: Subandroecious\n Subdioecious:\n text: Subdioecious\n Subgynoecious:\n text: Subgynoecious\n Synoecious:\n text: Synoecious\n Trimonoecious:\n text: Trimonoecious\n Trioecious:\n text: Trioecious\n Unisexual:\n text: Unisexual\n\nphysical combination of several instances of like material.
URI: nmdc:Pooling
classDiagram\n class Pooling\n BiosampleProcessing <|-- Pooling\n\n Pooling : alternative_identifiers\n\n Pooling : description\n\n Pooling : end_date\n\n Pooling : has_input\n\n Pooling --|> Biosample : has_input\n\n Pooling : has_output\n\n Pooling --|> NamedThing : has_output\n\n Pooling : id\n\n Pooling : name\n\n Pooling : protocol_link\n\n Pooling --|> Protocol : protocol_link\n\n Pooling : start_date\n\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 2\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 2\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: Pooling\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n minimum_cardinality: 2\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: Pooling\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n minimum_cardinality: 1\n maximum_cardinality: 1\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Pooling\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Pooling\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pooling\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pooling\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Pooling\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:ProcessedSample
classDiagram\n class ProcessedSample\n MaterialEntity <|-- ProcessedSample\n\n ProcessedSample : alternative_identifiers\n\n ProcessedSample : biomaterial_purity\n\n ProcessedSample --|> QuantityValue : biomaterial_purity\n\n ProcessedSample : description\n\n ProcessedSample : dna_absorb1\n\n ProcessedSample : dna_concentration\n\n ProcessedSample : external_database_identifiers\n\n ProcessedSample : id\n\n ProcessedSample : name\n\n ProcessedSample : nucleic_acid_concentration\n\n ProcessedSample --|> InstrumentValue : nucleic_acid_concentration\n\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\n- nucleic_acid_concentration\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n biomaterial_purity:\n name: biomaterial_purity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biomaterial_purity\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb1\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: dna_concentration\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n external_database_identifiers:\n name: external_database_identifiers\n description: Link to corresponding identifier in external database\n notes:\n - had tried ranges of external identifier and string\n comments:\n - The value of this field is always a registered CURIE\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - skos:closeMatch\n rank: 1000\n is_a: alternative_identifiers\n abstract: true\n multivalued: true\n alias: external_database_identifiers\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n nucleic_acid_concentration:\n name: nucleic_acid_concentration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: nucleic_acid_concentration\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: InstrumentValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ProcessedSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProcessedSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProcessedSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: ProcessedSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ProcessingInstitutionEnum
"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":"name: processing_institution_enum\nnotes:\n- This will become the range of processing_institution.omics processing\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n UCSD:\n text: UCSD\n meaning: https://ror.org/0168r3w48\n title: University of California, San Diego\n JGI:\n text: JGI\n meaning: https://ror.org/04xm1d337\n title: Joint Genome Institute\n EMSL:\n text: EMSL\n meaning: https://ror.org/04rc0xn13\n title: Environmental Molecular Sciences Laboratory\n notes:\n - replaces Environmental Molecular Science Laboratory\n - replaces Environmental Molecular Sciences Lab\n Battelle:\n text: Battelle\n meaning: https://ror.org/01h5tnr73\n title: Battelle Memorial Institute\n ANL:\n text: ANL\n meaning: https://ror.org/05gvnxz63\n title: Argonne National Laboratory\n\nURI: ProfilePositionEnum
"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":"name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n summit:\n text: summit\n shoulder:\n text: shoulder\n backslope:\n text: backslope\n footslope:\n text: footslope\n toeslope:\n text: toeslope\n\nThis is used to link a metaproteomics analysis workflow to a specific protein
URI: nmdc:ProteinQuantification
classDiagram\n class ProteinQuantification\n ProteinQuantification : all_proteins\n\n ProteinQuantification --|> GeneProduct : all_proteins\n\n ProteinQuantification : best_protein\n\n ProteinQuantification --|> GeneProduct : best_protein\n\n ProteinQuantification : peptide_sequence_count\n\n ProteinQuantification : protein_spectral_count\n\n ProteinQuantification : protein_sum_masic_abundance\n\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\nslot_usage:\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\nattributes:\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: all_proteins\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n peptide_sequence_count:\n name: peptide_sequence_count\n description: count of peptide sequences grouped to the best_protein\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_spectral_count:\n name: protein_spectral_count\n description: sum of filter passing MS2 spectra associated with the best protein\n within a given LC-MS/MS data file\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_spectral_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_sum_masic_abundance:\n name: protein_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the best protein from a given LC-MS/MS data file using the MASIC\n tool\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_sum_masic_abundance\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n\nURI: nmdc:Protocol
classDiagram\n class Protocol\n Protocol : name\n\n Protocol : url\n\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: Protocol\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Protocol\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nURI: QuadPosEnum
"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":"name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n North side:\n text: North side\n West side:\n text: West side\n South side:\n text: South side\n East side:\n text: East side\n\nURI: nmdc:QualityControlReport
classDiagram\n class QualityControlReport\n QualityControlReport : name\n\n QualityControlReport : status\n\n QualityControlReport --|> StatusEnum : status\n\n\nname: QualityControlReport\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- status\n- name\n\nname: QualityControlReport\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n status:\n name: status\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: status\n owner: QualityControlReport\n domain_of:\n - QualityControlReport\n range: StatusEnum\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: QualityControlReport\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nA simple quantity, e.g. 2cm
URI: nmdc:QuantityValue
classDiagram\n class QuantityValue\n AttributeValue <|-- QuantityValue\n\n QuantityValue : has_maximum_numeric_value\n\n QuantityValue : has_minimum_numeric_value\n\n QuantityValue : has_numeric_value\n\n QuantityValue : has_raw_value\n\n QuantityValue : has_unit\n\n QuantityValue : was_generated_by\n\n QuantityValue --|> Activity : was_generated_by\n\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_raw_value\n- has_unit\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n domain_of:\n - AttributeValue\n - QuantityValue\n has_unit:\n name: has_unit\n description: The unit of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n domain_of:\n - AttributeValue\n - QuantityValue\n has_unit:\n name: has_unit\n description: The unit of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\nattributes:\n has_maximum_numeric_value:\n name: has_maximum_numeric_value\n description: The maximum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_maximum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: float\n has_minimum_numeric_value:\n name: has_minimum_numeric_value\n description: The minimum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_minimum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: float\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: QuantityValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: QuantityValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n has_unit:\n name: has_unit\n description: The unit of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_unit\n owner: QuantityValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n range: unit\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: QuantityValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nAn individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters
URI: nmdc:Reaction
classDiagram\n class Reaction\n FunctionalAnnotationTerm <|-- Reaction\n\n Reaction : alternative_identifiers\n\n Reaction : description\n\n Reaction : direction\n\n Reaction : id\n\n Reaction : is_balanced\n\n Reaction : is_diastereoselective\n\n Reaction : is_fully_characterized\n\n Reaction : is_stereo\n\n Reaction : is_transport\n\n Reaction : left_participants\n\n Reaction --|> ReactionParticipant : left_participants\n\n Reaction : name\n\n Reaction : right_participants\n\n Reaction --|> ReactionParticipant : right_participants\n\n Reaction : smarts_string\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG.REACTION
RHEA
MetaCyc
EC
GO
MetaNetX
SEED
RetroRules
name: Reaction\nid_prefixes:\n- KEGG.REACTION\n- RHEA\n- MetaCyc\n- EC\n- GO\n- MetaNetX\n- SEED\n- RetroRules\ndescription: An individual biochemical transformation carried out by a functional\n unit of an organism, in which a collection of substrates are transformed into a\n collection of products. Can also represent transporters\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:MolecularActivity\nis_a: FunctionalAnnotationTerm\nslots:\n- direction\n- is_balanced\n- is_diastereoselective\n- is_fully_characterized\n- is_stereo\n- is_transport\n- left_participants\n- right_participants\n- smarts_string\n\nname: Reaction\nid_prefixes:\n- KEGG.REACTION\n- RHEA\n- MetaCyc\n- EC\n- GO\n- MetaNetX\n- SEED\n- RetroRules\ndescription: An individual biochemical transformation carried out by a functional\n unit of an organism, in which a collection of substrates are transformed into a\n collection of products. Can also represent transporters\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:MolecularActivity\nis_a: FunctionalAnnotationTerm\nattributes:\n direction:\n name: direction\n description: One of l->r, r->l, bidirectional, neutral\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: direction\n owner: Reaction\n domain_of:\n - Reaction\n range: string\n is_balanced:\n name: is_balanced\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_balanced\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_diastereoselective:\n name: is_diastereoselective\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_diastereoselective\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_fully_characterized:\n name: is_fully_characterized\n description: False if includes R-groups\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_fully_characterized\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_stereo:\n name: is_stereo\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_stereo\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_transport:\n name: is_transport\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_transport\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n left_participants:\n name: left_participants\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_participants\n multivalued: true\n alias: left_participants\n owner: Reaction\n domain_of:\n - Reaction\n range: ReactionParticipant\n right_participants:\n name: right_participants\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_participants\n multivalued: true\n alias: right_participants\n owner: Reaction\n domain_of:\n - Reaction\n range: ReactionParticipant\n smarts_string:\n name: smarts_string\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: smarts_string\n owner: Reaction\n domain_of:\n - Reaction\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Reaction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Reaction\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Reaction\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Reaction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:ReactionActivity
classDiagram\n class ReactionActivity\n ReactionActivity : material_input\n\n ReactionActivity --|> MaterialSample : material_input\n\n ReactionActivity : material_output\n\n ReactionActivity --|> MaterialSample : material_output\n\n ReactionActivity : reaction_aided_by\n\n ReactionActivity --|> LabDevice : reaction_aided_by\n\n ReactionActivity : reaction_temperature\n\n ReactionActivity : reaction_time\n\n ReactionActivity --|> QuantityValue : reaction_time\n\n\nname: ReactionActivity\ntitle: Reaction activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reaction-activity\nslots:\n- material_input\n- material_output\n- reaction_aided_by\n- reaction_temperature\n- reaction_time\nslot_usage:\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n domain_of:\n - ReactionActivity\n\nname: ReactionActivity\ntitle: Reaction activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reaction-activity\nslot_usage:\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n domain_of:\n - ReactionActivity\nattributes:\n material_input:\n name: material_input\n title: material input\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_input\n owner: ReactionActivity\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n range: MaterialSample\n material_output:\n name: material_output\n title: material output\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_output\n owner: ReactionActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\n reaction_aided_by:\n name: reaction_aided_by\n title: reaction aided by\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker\n rank: 1000\n alias: reaction_aided_by\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: LabDevice\n inlined: true\n reaction_temperature:\n name: reaction_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: reaction_temperature\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: string\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: reaction_time\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: QuantityValue\n inlined: true\n\nInstances of this link a reaction to a chemical entity participant
URI: nmdc:ReactionParticipant
classDiagram\n class ReactionParticipant\n ReactionParticipant : chemical\n\n ReactionParticipant --|> ChemicalEntity : chemical\n\n ReactionParticipant : stoichiometry\n\n\nname: ReactionParticipant\ndescription: Instances of this link a reaction to a chemical entity participant\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- chemical\n- stoichiometry\n\nname: ReactionParticipant\ndescription: Instances of this link a reaction to a chemical entity participant\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n chemical:\n name: chemical\n description: from reaction participant class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical\n owner: ReactionParticipant\n domain_of:\n - ReactionParticipant\n range: ChemicalEntity\n stoichiometry:\n name: stoichiometry\n description: from reaction participant class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stoichiometry\n owner: ReactionParticipant\n domain_of:\n - ReactionParticipant\n range: integer\n\nA workflow execution activity that performs taxonomy classification using sequencing reads
URI: nmdc:ReadBasedTaxonomyAnalysisActivity
classDiagram\n class ReadBasedTaxonomyAnalysisActivity\n WorkflowExecutionActivity <|-- ReadBasedTaxonomyAnalysisActivity\n\n ReadBasedTaxonomyAnalysisActivity : ended_at_time\n\n ReadBasedTaxonomyAnalysisActivity : execution_resource\n\n ReadBasedTaxonomyAnalysisActivity : git_url\n\n ReadBasedTaxonomyAnalysisActivity : has_input\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : has_input\n\n ReadBasedTaxonomyAnalysisActivity : has_output\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : has_output\n\n ReadBasedTaxonomyAnalysisActivity : id\n\n ReadBasedTaxonomyAnalysisActivity : name\n\n ReadBasedTaxonomyAnalysisActivity : part_of\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : part_of\n\n ReadBasedTaxonomyAnalysisActivity : started_at_time\n\n ReadBasedTaxonomyAnalysisActivity : type\n\n ReadBasedTaxonomyAnalysisActivity : used\n\n ReadBasedTaxonomyAnalysisActivity : version\n\n ReadBasedTaxonomyAnalysisActivity : was_informed_by\n\n ReadBasedTaxonomyAnalysisActivity --|> Activity : was_informed_by\n\n\nname: ReadBasedTaxonomyAnalysisActivity\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ReadBasedTaxonomyAnalysisActivity\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nA workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
URI: nmdc:ReadQcAnalysisActivity
classDiagram\n class ReadQcAnalysisActivity\n WorkflowExecutionActivity <|-- ReadQcAnalysisActivity\n\n ReadQcAnalysisActivity : ended_at_time\n\n ReadQcAnalysisActivity : execution_resource\n\n ReadQcAnalysisActivity : git_url\n\n ReadQcAnalysisActivity : has_input\n\n ReadQcAnalysisActivity --|> NamedThing : has_input\n\n ReadQcAnalysisActivity : has_output\n\n ReadQcAnalysisActivity --|> NamedThing : has_output\n\n ReadQcAnalysisActivity : id\n\n ReadQcAnalysisActivity : input_base_count\n\n ReadQcAnalysisActivity : input_read_bases\n\n ReadQcAnalysisActivity : input_read_count\n\n ReadQcAnalysisActivity : name\n\n ReadQcAnalysisActivity : output_base_count\n\n ReadQcAnalysisActivity : output_read_bases\n\n ReadQcAnalysisActivity : output_read_count\n\n ReadQcAnalysisActivity : part_of\n\n ReadQcAnalysisActivity --|> NamedThing : part_of\n\n ReadQcAnalysisActivity : started_at_time\n\n ReadQcAnalysisActivity : type\n\n ReadQcAnalysisActivity : used\n\n ReadQcAnalysisActivity : version\n\n ReadQcAnalysisActivity : was_informed_by\n\n ReadQcAnalysisActivity --|> Activity : was_informed_by\n\n\nname: ReadQcAnalysisActivity\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- input_read_count\n- input_base_count\n- output_read_count\n- output_base_count\n- input_read_bases\n- output_read_bases\n- version\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ReadQcAnalysisActivity\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: ReadQcAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n input_read_count:\n name: input_read_count\n description: The sequence count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_read_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n input_base_count:\n name: input_base_count\n description: The nucleotide base count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_base_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_read_count:\n name: output_read_count\n description: After QC analysis sequence count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_read_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_base_count:\n name: output_base_count\n description: After QC analysis nucleotide base count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_base_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n input_read_bases:\n name: input_read_bases\n description: 'TODO '\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_read_bases\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_read_bases:\n name: output_read_bases\n description: TODO\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: output_read_bases\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: ReadQcAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: ReadQcAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: ReadQcAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ReadQcAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadQcAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: RelSampLocEnum
"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":"name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n edge of car:\n text: edge of car\n center of car:\n text: center of car\n under a seat:\n text: under a seat\n\nURI: RnaSampleFormatEnum
"},{"location":"RnaSampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RnaSampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RnaSampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RnaSampleFormatEnum/#schema-source","title":"Schema Source","text":"name: rna_sample_format_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: RoomCondtEnum
"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":"name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n visible signs of mold/mildew:\n text: visible signs of mold/mildew\n\nURI: RoomConnectedEnum
"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":"name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n office:\n text: office\n stairwell:\n text: stairwell\n\nURI: RoomLocEnum
"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":"name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n corner room:\n text: corner room\n interior room:\n text: interior room\n exterior wall:\n text: exterior wall\n\nURI: RoomSampPosEnum
"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":"name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north corner:\n text: north corner\n south corner:\n text: south corner\n west corner:\n text: west corner\n east corner:\n text: east corner\n northeast corner:\n text: northeast corner\n northwest corner:\n text: northwest corner\n southeast corner:\n text: southeast corner\n southwest corner:\n text: southwest corner\n center:\n text: center\n\nURI: RoomTypeEnum
"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":"name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n private office:\n text: private office\n open office:\n text: open office\n stairwell:\n text: stairwell\n ',restroom':\n text: ',restroom'\n lobby:\n text: lobby\n vestibule:\n text: vestibule\n mechanical or electrical room:\n text: mechanical or electrical room\n data center:\n text: data center\n laboratory_wet:\n text: laboratory_wet\n laboratory_dry:\n text: laboratory_dry\n gymnasium:\n text: gymnasium\n natatorium:\n text: natatorium\n auditorium:\n text: auditorium\n lockers:\n text: lockers\n cafe:\n text: cafe\n warehouse:\n text: warehouse\n\nURI: SampCaptStatusEnum
"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":"name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n active surveillance in response to an outbreak:\n text: active surveillance in response to an outbreak\n active surveillance not initiated by an outbreak:\n text: active surveillance not initiated by an outbreak\n farm sample:\n text: farm sample\n market sample:\n text: market sample\n other:\n text: other\n\nURI: SampCollectPointEnum
"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":"name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n well:\n text: well\n test well:\n text: test well\n drilling rig:\n text: drilling rig\n wellhead:\n text: wellhead\n separator:\n text: separator\n storage tank:\n text: storage tank\n other:\n text: other\n\nURI: SampDisStageEnum
"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":"name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dissemination:\n text: dissemination\n growth and reproduction:\n text: growth and reproduction\n infection:\n text: infection\n inoculation:\n text: inoculation\n penetration:\n text: penetration\n other:\n text: other\n\nURI: SampFloorEnum
"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":"name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 1st floor:\n text: 1st floor\n 2nd floor:\n text: 2nd floor\n basement:\n text: basement\n lobby:\n text: lobby\n\nURI: SampMdEnum
"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":"name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DF:\n text: DF\n RT:\n text: RT\n KB:\n text: KB\n MSL:\n text: MSL\n other:\n text: other\n\nURI: SampSubtypeEnum
"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":"name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n oil phase:\n text: oil phase\n water phase:\n text: water phase\n biofilm:\n text: biofilm\n not applicable:\n text: not applicable\n other:\n text: other\n\nURI: SampWeatherEnum
"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":"name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clear sky:\n text: clear sky\n cloudy:\n text: cloudy\n foggy:\n text: foggy\n hail:\n text: hail\n rain:\n text: rain\n snow:\n text: snow\n sleet:\n text: sleet\n sunny:\n text: sunny\n windy:\n text: windy\n\nSubset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.
URI: SampleSubset
"},{"location":"SampleSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleSubset/#schema-source","title":"Schema Source","text":"Biological source material which can be characterized by an experiment.
"},{"location":"SampleSubset/#omicsprocessing","title":"OmicsProcessing","text":"The methods and processes used to generate omics data from a biosample or organism.
"},{"location":"SampleSubset/#study","title":"Study","text":"A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
"},{"location":"SampleTypeEnum/","title":"Enum: SampleTypeEnum","text":"URI: SampleTypeEnum
"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None water_extract_soil None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":"name: sample_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n soil:\n text: soil\n water_extract_soil:\n text: water_extract_soil\n\nURI: SamplingMethodEnum
"},{"location":"SamplingMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description weighing None"},{"location":"SamplingMethodEnum/#slots","title":"Slots","text":"Name Description sampling_method"},{"location":"SamplingMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplingMethodEnum/#schema-source","title":"Schema Source","text":"name: SamplingMethodEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n weighing:\n text: weighing\n title: Weighing\n\nURI: SeasonUseEnum
"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":"name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Spring:\n text: Spring\n Summer:\n text: Summer\n Fall:\n text: Fall\n Winter:\n text: Winter\n\nURI: SedimentTypeEnum
"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":"name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n biogenous:\n text: biogenous\n cosmogenous:\n text: cosmogenous\n hydrogenous:\n text: hydrogenous\n lithogenous:\n text: lithogenous\n\nURI: Sequencing
"},{"location":"Sequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sequencing/#schema-source","title":"Schema Source","text":"URI: ShadingDeviceCondEnum
"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":"name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: ShadingDeviceTypeEnum
"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bahama shutters:\n text: bahama shutters\n exterior roll blind:\n text: exterior roll blind\n gambrel awning:\n text: gambrel awning\n hood awning:\n text: hood awning\n porchroller awning:\n text: porchroller awning\n sarasota shutters:\n text: sarasota shutters\n slatted aluminum:\n text: slatted aluminum\n solid aluminum awning:\n text: solid aluminum awning\n sun screen:\n text: sun screen\n tree:\n text: tree\n trellis:\n text: trellis\n venetian awning:\n text: venetian awning\n\nURI: nmdc:Site
classDiagram\n class Site\n MaterialEntity <|-- Site\n\n\n Site <|-- FieldResearchSite\n\n\n Site : alternative_identifiers\n\n Site : description\n\n Site : id\n\n Site : name\n\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Site\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Site\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Site\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Site\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: SoilHorizonEnum
"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":"name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n O horizon:\n text: O horizon\n A horizon:\n text: A horizon\n E horizon:\n text: E horizon\n B horizon:\n text: B horizon\n C horizon:\n text: C horizon\n R layer:\n text: R layer\n Permafrost:\n text: Permafrost\n M horizon:\n text: M horizon\n\nURI: SolventEnum
"},{"location":"SolventEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description deionized_water None methanol CHEBI:17790 chloroform CHEBI:35255"},{"location":"SolventEnum/#slots","title":"Slots","text":"Name Description dissolution_reagent"},{"location":"SolventEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SolventEnum/#schema-source","title":"Schema Source","text":"name: SolventEnum\ntitle: Solvent enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n deionized_water:\n text: deionized_water\n title: Deionized water\n broad_mappings:\n - CHEBI:15377\n methanol:\n text: methanol\n meaning: CHEBI:17790\n title: Methanol\n chloroform:\n text: chloroform\n meaning: CHEBI:35255\n title: Chloroform\n\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: SpecificEnum
"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":"name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n photos:\n text: photos\n\nURI: SrDepEnvEnum
"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":"name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Lacustine:\n text: Lacustine\n Fluvioldeltaic:\n text: Fluvioldeltaic\n Fluviomarine:\n text: Fluviomarine\n Marine:\n text: Marine\n other:\n text: other\n\nURI: SrGeolAgeEnum
"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: SrKerogTypeEnum
"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":"name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Type I:\n text: Type I\n Type II:\n text: Type II\n Type III:\n text: Type III\n Type IV:\n text: Type IV\n other:\n text: other\n\nURI: SrLithologyEnum
"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":"name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Clastic:\n text: Clastic\n Carbonate:\n text: Carbonate\n Coal:\n text: Coal\n Biosilicieous:\n text: Biosilicieous\n other:\n text: other\n\nURI: StatusEnum
"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description status"},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":"name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n pass:\n text: pass\n fail:\n text: fail\n\nA character string
URI: xsd:string
base: str
uri: xsd:string
A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
URI: nmdc:Study
classDiagram\n class Study\n NamedThing <|-- Study\n\n Study : alternative_descriptions\n\n Study : alternative_identifiers\n\n Study : alternative_names\n\n Study : alternative_titles\n\n Study : award_dois\n\n Study : dataset_dois\n\n Study : description\n\n Study : ecosystem\n\n Study : ecosystem_category\n\n Study : ecosystem_subtype\n\n Study : ecosystem_type\n\n Study : emsl_project_dois\n\n Study : ess_dive_datasets\n\n Study : funding_sources\n\n Study : gnps_task_identifiers\n\n Study : gold_study_identifiers\n\n Study : has_credit_associations\n\n Study --|> CreditAssociation : has_credit_associations\n\n Study : id\n\n Study : insdc_bioproject_identifiers\n\n Study : jgi_portal_study_identifiers\n\n Study : massive_study_identifiers\n\n Study : mgnify_project_identifiers\n\n Study : name\n\n Study : neon_study_identifiers\n\n Study : notes\n\n Study : objective\n\n Study : part_of\n\n Study --|> Study : part_of\n\n Study : principal_investigator\n\n Study --|> PersonValue : principal_investigator\n\n Study : publication_dois\n\n Study : publications\n\n Study : related_identifiers\n\n Study : relevant_protocols\n\n Study : specific_ecosystem\n\n Study : study_category\n\n Study --|> StudyCategoryEnum : study_category\n\n Study : study_image\n\n Study --|> ImageValue : study_image\n\n Study : title\n\n Study : type\n\n Study : websites\n\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research inititative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_dois\n- neon_study_identifiers\n- jgi_portal_study_identifiers\n- id\n- alternative_identifiers\n- gnps_task_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- description\n- award_dois\n- dataset_dois\n- publication_dois\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- ess_dive_datasets\n- funding_sources\n- gold_study_identifiers\n- has_credit_associations\n- study_category\n- insdc_bioproject_identifiers\n- massive_study_identifiers\n- mgnify_project_identifiers\n- notes\n- objective\n- part_of\n- principal_investigator\n- publications\n- related_identifiers\n- relevant_protocols\n- specific_ecosystem\n- study_image\n- title\n- type\n- websites\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n domain_of:\n - Study\n - PersonValue\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n domain_of:\n - Study\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n domain_of:\n - Study\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n domain_of:\n - Study\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n domain_of:\n - Study\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research inititative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n domain_of:\n - Study\n - PersonValue\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n domain_of:\n - Study\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n domain_of:\n - Study\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n domain_of:\n - Study\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n domain_of:\n - Study\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\nattributes:\n emsl_project_dois:\n name: emsl_project_dois\n description: One or more DOIs that links to an EMSL Research Campaign page.\n title: EMSL Project DOI\n todos:\n - Make as a subproperty of award_dois\n examples:\n - value: doi:10.46936/intm.proj.2021.6014\n description: emsl_project_dois link to the document outlining the EMSL specific\n award for the project. Should not be used to link to datasets or publications.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n mixins:\n - emsl_identifiers\n multivalued: true\n alias: emsl_project_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n neon_study_identifiers:\n name: neon_study_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - neon_identifiers\n multivalued: true\n alias: neon_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n jgi_portal_study_identifiers:\n name: jgi_portal_study_identifiers\n id_prefixes:\n - jgi.proposal\n description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD\n API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n title: JGI Portal Study identifiers\n comments:\n - Could this could be considered a related identifier?\n - Curie suffix is the Site Award Number from an OSTI award page\n - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n study identifier gold:Gs0154044\n - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n examples:\n - value: jgi.proposal:507130\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - jgi_portal_identifiers\n multivalued: true\n alias: jgi_portal_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^jgi.proposal:\\d+$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Study\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Study\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n gnps_task_identifiers:\n name: gnps_task_identifiers\n description: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\n title: GNPS task identifiers\n comments:\n - this could be considered a related identifier, as the metabolomics progress\n and results aren't a study per se\n - this identifier was registered with bioregistry but not identifiers.org\n examples:\n - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gnps_identifiers\n multivalued: true\n alias: gnps_task_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^gnps\\.task:[a-f0-9]+$\n alternative_descriptions:\n name: alternative_descriptions\n description: A list of alternative descriptions for the entity. The distinction\n between description and alternative descriptions is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_descriptions\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_names\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_titles:\n name: alternative_titles\n description: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n rank: 1000\n multivalued: true\n alias: alternative_titles\n owner: Study\n domain_of:\n - Study\n range: string\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Study\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n award_dois:\n name: award_dois\n description: One or more DOIs that links a study, or similar entiry, to information\n about the funding authority.\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: award_dois link to to an award document. Should not be used to\n link to datasets or publications. For example, doi:10.15485/1577267 is not\n an award doi, but a dataset doi.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: award_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n dataset_dois:\n name: dataset_dois\n description: One or more DOIs that links a study, or similar entity, to the generated\n data.\n examples:\n - value: doi:10.15485/1577267\n description: dataset_dois link to data encoded in a defined structure (as defined\n by DataCite). Should not be used to link to publications or administrative\n information like funding requests or awards.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: dataset_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n publication_dois:\n name: publication_dois\n description: One or more DOIs that links a study, or similar entity, to a publication.\n examples:\n - value: doi:10.1126/science.1058040\n description: publication_dois link to a prose document, preferably a peer-reviewed\n journal article. Should not be used to link to datasets or administrative\n information like funding requests or awards\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: publication_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ess_dive_datasets:\n name: ess_dive_datasets\n description: List of ESS-DIVE dataset DOIs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: ess_dive_datasets\n owner: Study\n domain_of:\n - Study\n range: string\n funding_sources:\n name: funding_sources\n description: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process\n applications and award funds to the chosen qualified applicants.\n comments:\n - Include only the name of the funding organization and the award or contract\n number.\n examples:\n - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n - value: U.S. Department of Energy, Office of Science, Office of Biological and\n Environmental Research (BER) under contract DE-AC05-00OR2275\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C39409\n rank: 1000\n multivalued: true\n alias: funding_sources\n owner: Study\n domain_of:\n - Study\n range: string\n gold_study_identifiers:\n name: gold_study_identifiers\n description: identifiers for corresponding project(s) in GOLD\n title: GOLD Study Identifiers\n comments:\n - uses the prefix GS (but possibly in a different case)\n examples:\n - value: https://bioregistry.io/gold:Gs0110115\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/studies\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^gold:Gs[0-9]+$\n has_credit_associations:\n name: has_credit_associations\n annotations:\n display_hint:\n tag: display_hint\n value: Other researchers associated with this study.\n description: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\n notes:\n - 'had just been \"inlined: true\"'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Study\n slot_uri: prov:qualifiedAssociation\n multivalued: true\n alias: has_credit_associations\n owner: Study\n domain_of:\n - Study\n range: CreditAssociation\n inlined: true\n inlined_as_list: true\n study_category:\n name: study_category\n description: The type of research initiative\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_category\n owner: Study\n domain_of:\n - Study\n range: StudyCategoryEnum\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n multivalued: true\n alias: insdc_bioproject_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n massive_study_identifiers:\n name: massive_study_identifiers\n description: identifiers for corresponding study in MASSIVE\n todos:\n - prefix not defined yet\n examples:\n - value: MASSIVE:MSV000090886\n description: MASSIVE id for MASSIVE's metabolomics analysis of Gb0305843, resolvable\n with prefix http://identifiers.org/massive/\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=83574f41458a4b259621d5c32a4d82f9\n rank: 1000\n is_a: study_identifiers\n mixins:\n - massive_identifiers\n multivalued: true\n alias: massive_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: '^MASSIVE:'\n mgnify_project_identifiers:\n name: mgnify_project_identifiers\n description: identifiers for corresponding project in MGnify\n examples:\n - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - mgnify_identifiers\n multivalued: true\n alias: mgnify_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n description: from study class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: notes\n owner: Study\n domain_of:\n - Study\n range: string\n objective:\n name: objective\n description: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - SIO:000337\n rank: 1000\n multivalued: false\n alias: objective\n owner: Study\n domain_of:\n - Study\n range: string\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: Study\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n is_a: attribute\n alias: principal_investigator\n owner: Study\n domain_of:\n - Study\n - OmicsProcessing\n range: PersonValue\n publications:\n name: publications\n description: A list of publications that are associated with the entity. The publications\n SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: publications\n owner: Study\n domain_of:\n - Study\n range: string\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n title: Related Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: related_identifiers\n owner: Study\n domain_of:\n - Study\n range: string\n relevant_protocols:\n name: relevant_protocols\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: relevant_protocols\n owner: Study\n domain_of:\n - Study\n range: string\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n study_image:\n name: study_image\n description: Links a study to one or more images.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Study\n multivalued: true\n alias: study_image\n owner: Study\n domain_of:\n - Study\n range: ImageValue\n inlined: true\n title:\n name: title\n description: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the\n GOLD system has assigned a name/label. However, for display purposes, we may\n also wish the capture the title of the proposal that was used to fund the study.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:title\n rank: 1000\n alias: title\n owner: Study\n domain_of:\n - Study\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: Study\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n description: A list of websites that are associated with the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: websites\n owner: Study\n domain_of:\n - Study\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Study\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nURI: StudyCategoryEnum
"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":"name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n research_study:\n text: research_study\n description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n experiment.\n exact_mappings:\n - SIO:001066\n - NCIT:C63536\n - ISA:Study\n close_mappings:\n - OBI:0000355\n consortium:\n text: consortium\n description: A group formed to undertake a venture that is beyond the capabilities\n of the individual members. Each member of the consortium brings a high level\n of expertise in a specific area to ensure the successful completion of the project.\n comments:\n - A consortium has collections of data, those data do not come from a hypothesis-driven\n experiment.\n exact_mappings:\n - NCIT:C61538\n\nURI: SubstructureTypeEnum
"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":"name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crawlspace:\n text: crawlspace\n slab on grade:\n text: slab on grade\n basement:\n text: basement\n\nURI: SurfAirContEnum
"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":"name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dust:\n text: dust\n organic matter:\n text: organic matter\n particulate matter:\n text: particulate matter\n volatile organic compounds:\n text: volatile organic compounds\n biological contaminants:\n text: biological contaminants\n radon:\n text: radon\n nutrients:\n text: nutrients\n biocides:\n text: biocides\n\nURI: SurfMaterialEnum
"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":"name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n adobe:\n text: adobe\n carpet:\n text: carpet\n cinder blocks:\n text: cinder blocks\n concrete:\n text: concrete\n hay bales:\n text: hay bales\n glass:\n text: glass\n metal:\n text: metal\n paint:\n text: paint\n plastic:\n text: plastic\n stainless steel:\n text: stainless steel\n stone:\n text: stone\n stucco:\n text: stucco\n tile:\n text: tile\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nA basic string value
URI: nmdc:TextValue
classDiagram\n class TextValue\n AttributeValue <|-- TextValue\n\n TextValue : has_raw_value\n\n TextValue : language\n\n TextValue : was_generated_by\n\n TextValue --|> Activity : was_generated_by\n\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n language:\n name: language\n description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: language\n owner: TextValue\n domain_of:\n - TextValue\n range: language code\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: TextValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: TextValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: TidalStageEnum
"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":"name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low tide:\n text: low tide\n ebb tide:\n text: ebb tide\n flood tide:\n text: flood tide\n high tide:\n text: high tide\n\nURI: TillageEnum
"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":"name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drill:\n text: drill\n cutting disc:\n text: cutting disc\n ridge till:\n text: ridge till\n strip tillage:\n text: strip tillage\n zonal tillage:\n text: zonal tillage\n chisel:\n text: chisel\n tined:\n text: tined\n mouldboard:\n text: mouldboard\n disc plough:\n text: disc plough\n\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
A value that is a timestamp. The range should be ISO-8601
URI: nmdc:TimestampValue
classDiagram\n class TimestampValue\n AttributeValue <|-- TimestampValue\n\n TimestampValue : has_raw_value\n\n TimestampValue : was_generated_by\n\n TimestampValue --|> Activity : was_generated_by\n\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: TimestampValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: TimestampValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: TrainLineEnum
"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":"name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n red:\n text: red\n green:\n text: green\n orange:\n text: orange\n\nURI: TrainStatLocEnum
"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":"name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n south station above ground:\n text: south station above ground\n south station underground:\n text: south station underground\n south station amtrak:\n text: south station amtrak\n forest hills:\n text: forest hills\n riverside:\n text: riverside\n\nURI: TrainStopLocEnum
"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":"name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n end:\n text: end\n mid:\n text: mid\n downtown:\n text: downtown\n\nURI: xsd:string
base: str
uri: xsd:string
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
A value that is a string that conforms to URL syntax
URI: nmdc:UrlValue
classDiagram\n class UrlValue\n AttributeValue <|-- UrlValue\n\n UrlValue : has_raw_value\n\n UrlValue : was_generated_by\n\n UrlValue --|> Activity : was_generated_by\n\n\nname: UrlValue\ndescription: A value that is a string that conforms to URL syntax\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\n\nname: UrlValue\ndescription: A value that is a string that conforms to URL syntax\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: UrlValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: UrlValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: VisMediaEnum
"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":"name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n photos:\n text: photos\n videos:\n text: videos\n commonly of the building:\n text: commonly of the building\n site context (adjacent buildings, vegetation, terrain, streets):\n text: site context (adjacent buildings, vegetation, terrain, streets)\n interiors:\n text: interiors\n equipment:\n text: equipment\n 3D scans:\n text: 3D scans\n\nURI: WallConstTypeEnum
"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":"name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n frame construction:\n text: frame construction\n joisted masonry:\n text: joisted masonry\n light noncombustible:\n text: light noncombustible\n masonry noncombustible:\n text: masonry noncombustible\n modified fire resistive:\n text: modified fire resistive\n fire resistive:\n text: fire resistive\n\nURI: WallFinishMatEnum
"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":"name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plaster:\n text: plaster\n gypsum plaster:\n text: gypsum plaster\n veneer plaster:\n text: veneer plaster\n gypsum board:\n text: gypsum board\n tile:\n text: tile\n terrazzo:\n text: terrazzo\n stone facing:\n text: stone facing\n acoustical treatment:\n text: acoustical treatment\n wood:\n text: wood\n metal:\n text: metal\n masonry:\n text: masonry\n\nURI: WallLocEnum
"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":"name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WallSurfTreatmentEnum
"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":"name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n painted:\n text: painted\n wall paper:\n text: wall paper\n no treatment:\n text: no treatment\n paneling:\n text: paneling\n stucco:\n text: stucco\n fabric:\n text: fabric\n\nURI: WallTextureEnum
"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":"name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n ? ''\n : text: ''\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: WaterFeatTypeEnum
"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":"name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fountain:\n text: fountain\n pool:\n text: pool\n standing feature:\n text: standing feature\n stream:\n text: stream\n waterfall:\n text: waterfall\n\nURI: WeekdayEnum
"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":"name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Monday:\n text: Monday\n Tuesday:\n text: Tuesday\n Wednesday:\n text: Wednesday\n Thursday:\n text: Thursday\n Friday:\n text: Friday\n Saturday:\n text: Saturday\n Sunday:\n text: Sunday\n\nURI: WindowCondEnum
"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":"name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: WindowCoverEnum
"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":"name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n blinds:\n text: blinds\n curtains:\n text: curtains\n none:\n text: none\n\nURI: WindowHorizPosEnum
"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":"name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n left:\n text: left\n middle:\n text: middle\n right:\n text: right\n\nURI: WindowLocEnum
"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":"name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WindowMatEnum
"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":"name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clad:\n text: clad\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: WindowTypeEnum
"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":"name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n single-hung sash window:\n text: single-hung sash window\n horizontal sash window:\n text: horizontal sash window\n fixed window:\n text: fixed window\n\nURI: WindowVertPosEnum
"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":"name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bottom:\n text: bottom\n middle:\n text: middle\n top:\n text: top\n low:\n text: low\n high:\n text: high\n\nRepresents an instance of an execution of a particular workflow
URI: nmdc:WorkflowExecutionActivity
classDiagram\n class WorkflowExecutionActivity\n Activity <|-- WorkflowExecutionActivity\n\n\n WorkflowExecutionActivity <|-- MetagenomeAssembly\n WorkflowExecutionActivity <|-- MetatranscriptomeAssembly\n WorkflowExecutionActivity <|-- MetagenomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeActivity\n WorkflowExecutionActivity <|-- MagsAnalysisActivity\n WorkflowExecutionActivity <|-- MetagenomeSequencingActivity\n WorkflowExecutionActivity <|-- ReadQcAnalysisActivity\n WorkflowExecutionActivity <|-- ReadBasedTaxonomyAnalysisActivity\n WorkflowExecutionActivity <|-- MetabolomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetaproteomicsAnalysisActivity\n WorkflowExecutionActivity <|-- NomAnalysisActivity\n\n\n WorkflowExecutionActivity : ended_at_time\n\n WorkflowExecutionActivity : execution_resource\n\n WorkflowExecutionActivity : git_url\n\n WorkflowExecutionActivity : has_input\n\n WorkflowExecutionActivity --|> NamedThing : has_input\n\n WorkflowExecutionActivity : has_output\n\n WorkflowExecutionActivity --|> NamedThing : has_output\n\n WorkflowExecutionActivity : id\n\n WorkflowExecutionActivity : name\n\n WorkflowExecutionActivity : part_of\n\n WorkflowExecutionActivity --|> NamedThing : part_of\n\n WorkflowExecutionActivity : started_at_time\n\n WorkflowExecutionActivity : type\n\n WorkflowExecutionActivity : used\n\n WorkflowExecutionActivity : version\n\n WorkflowExecutionActivity : was_informed_by\n\n WorkflowExecutionActivity --|> Activity : was_informed_by\n\n\nname: WorkflowExecutionActivity\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) activities is a distinct run with start and\n stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: Activity\nslots:\n- execution_resource\n- git_url\n- has_input\n- has_output\n- part_of\n- type\n- version\nslot_usage:\n started_at_time:\n name: started_at_time\n domain_of:\n - Activity\n required: true\n ended_at_time:\n name: ended_at_time\n domain_of:\n - Activity\n required: true\n git_url:\n name: git_url\n domain_of:\n - WorkflowExecutionActivity\n required: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n execution_resource:\n name: execution_resource\n domain_of:\n - WorkflowExecutionActivity\n required: true\n type:\n name: type\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: WorkflowExecutionActivity\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) activities is a distinct run with start and\n stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: Activity\nslot_usage:\n started_at_time:\n name: started_at_time\n domain_of:\n - Activity\n required: true\n ended_at_time:\n name: ended_at_time\n domain_of:\n - Activity\n required: true\n git_url:\n name: git_url\n domain_of:\n - WorkflowExecutionActivity\n required: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n execution_resource:\n name: execution_resource\n domain_of:\n - WorkflowExecutionActivity\n required: true\n type:\n name: type\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: WorkflowExecutionActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: WorkflowExecutionActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: WorkflowExecutionActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: WorkflowExecutionActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: WorkflowExecutionActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: WorkflowExecutionActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n\nSubset consisting of just the workflow execution activities
URI: WorkflowSubset
"},{"location":"WorkflowSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowSubset/#schema-source","title":"Schema Source","text":"A workflow execution activity that uses computational binning tools to group assembled contigs into genomes
"},{"location":"WorkflowSubset/#metabolomicsanalysisactivity","title":"MetabolomicsAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#metagenomeannotationactivity","title":"MetagenomeAnnotationActivity","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
"},{"location":"WorkflowSubset/#metagenomeassembly","title":"MetagenomeAssembly","text":"A workflow execution activity that converts sequencing reads into an assembled metagenome.
"},{"location":"WorkflowSubset/#metagenomesequencingactivity","title":"MetagenomeSequencingActivity","text":"Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
"},{"location":"WorkflowSubset/#metaproteomicsanalysisactivity","title":"MetaproteomicsAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#metatranscriptomeactivity","title":"MetatranscriptomeActivity","text":"A metatranscriptome activity that e.g. pools assembly and annotation activity.
"},{"location":"WorkflowSubset/#metatranscriptomeannotationactivity","title":"MetatranscriptomeAnnotationActivity","text":"None
"},{"location":"WorkflowSubset/#metatranscriptomeassembly","title":"MetatranscriptomeAssembly","text":"None
"},{"location":"WorkflowSubset/#nomanalysisactivity","title":"NomAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#readbasedtaxonomyanalysisactivity","title":"ReadBasedTaxonomyAnalysisActivity","text":"A workflow execution activity that performs taxonomy classification using sequencing reads
"},{"location":"WorkflowSubset/#readqcanalysisactivity","title":"ReadQcAnalysisActivity","text":"A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
"},{"location":"WorkflowSubset/#workflowexecutionactivity","title":"WorkflowExecutionActivity","text":"Represents an instance of an execution of a particular workflow
"},{"location":"YesNoEnum/","title":"Enum: YesNoEnum","text":"replaces DnaDnaseEnum and DnaseRnaEnum
URI: YesNoEnum
"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dnase_rna dna_dnase"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":"name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 'no':\n text: 'no'\n 'yes':\n text: 'yes'\n\nSchema resources for the National Microbiome Data Collaborative (NMDC)
"},{"location":"abs_air_humidity/","title":"Slot: abs_air_humidity","text":"Actual mass of water vapor - mh20 - present in the air water vapor mixture
URI: MIXS:0000122
"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":"name: abs_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nmultivalued: false\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of workflow activities.
URI: nmdc:activity_set
"},{"location":"activity_set/#inheritance","title":"Inheritance","text":"Range: WorkflowExecutionActivity
Multivalued: True
name: activity_set\ndescription: This property links a database object to the set of workflow activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: activity_set\ndomain_of:\n- Database\nrange: WorkflowExecutionActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:activity_speed
"},{"location":"activity_speed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_speed/#properties","title":"Properties","text":"name: activity_speed\ntitle: activity speed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shake_speed\nrank: 1000\nalias: activity_speed\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:activity_temperature
"},{"location":"activity_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_temperature/#properties","title":"Properties","text":"name: activity_temperature\ntodos:\n- constrain units\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: activity_temperature\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:activity_time
"},{"location":"activity_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_time/#properties","title":"Properties","text":"name: activity_time\ntitle: activity time\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shake_time\nrank: 1000\nalias: activity_time\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nThe date on which the information was added to the database.
URI: nmdc:add_date
"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"add_date/#properties","title":"Properties","text":"name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: string\n\nAdditional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001009
"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":"name: add_recov_method\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one of\n them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nmultivalued: false\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
URI: MIXS:0000300
"},{"location":"additional_info/#inheritance","title":"Inheritance","text":"name: additional_info\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nmultivalued: false\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe street name and building number where the sampling occurred.
URI: MIXS:0000218
"},{"location":"address/#inheritance","title":"Inheritance","text":"name: address\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nmultivalued: false\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of rooms (room number, room name) immediately adjacent to the sampling room
URI: MIXS:0000219
"},{"location":"adj_room/#inheritance","title":"Inheritance","text":"name: adj_room\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nmultivalued: false\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\n\nAerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
URI: MIXS:0000773
"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":"name: aero_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nmultivalued: false\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\n\nAddition of fertilizers, pesticides, etc. - amount and time of applications
URI: MIXS:0000639
"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: agrochem_addition\nannotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nmultivalued: true\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
URI: MIXS:0000108
"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_PM_concen\nannotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nmultivalued: true\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\n\nTemperature of the air at the time of sampling
URI: MIXS:0000124
"},{"location":"air_temp/#inheritance","title":"Inheritance","text":"name: air_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nmultivalued: false\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens
URI: MIXS:0000551
"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nmultivalued: true\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAluminum saturation (esp. For tropical soils)
URI: MIXS:0000607
"},{"location":"al_sat/#inheritance","title":"Inheritance","text":"name: al_sat\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nmultivalued: false\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining Al saturation
URI: MIXS:0000324
"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":"name: al_sat_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nmultivalued: false\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nAlkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
URI: MIXS:0000421
"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":"name: alkalinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nmultivalued: false\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod used for alkalinity measurement
URI: MIXS:0000298
"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":"name: alkalinity_method\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nmultivalued: false\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of alkyl diethers
URI: MIXS:0000490
"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":"name: alkyl_diethers\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nmultivalued: false\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nthe list of protein identifiers that are associated with the peptide sequence
URI: nmdc:all_proteins
"},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"all_proteins/#properties","title":"Properties","text":"Range: GeneProduct
Multivalued: True
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nAltitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air
URI: MIXS:0000094
"},{"location":"alt/#inheritance","title":"Inheritance","text":"name: alt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n layers and clouds. It is used to measure the height of an object which is above\n the earth's surface. In this context, the altitude measurement is the vertical distance\n between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nmultivalued: false\nalias: alt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOne or more other email addresses for an entity.
URI: nmdc:alternate_emails
"},{"location":"alternate_emails/#properties","title":"Properties","text":"name: alternate_emails\ndescription: One or more other email addresses for an entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternate_emails\nrange: string\n\nA list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.
URI: nmdc:alternative_descriptions
"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\n\nA list of alternative identifiers for the entity.
URI: nmdc:alternative_identifiers
"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: alternative_identifiers\ndomain_of:\n- Biosample\n- Study\n- NamedThing\n- MetaboliteQuantification\nrange: uriorcurie\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nA list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.
URI: nmdc:alternative_names
"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"alternative_names/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nmultivalued: true\nalias: alternative_names\ndomain_of:\n- Study\nrange: string\n\nA list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.
URI: nmdc:alternative_titles
"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nmultivalued: true\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\n\nMeasurement of aminopeptidase activity
URI: MIXS:0000172
"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":"name: aminopept_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nmultivalued: false\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of ammonium in the sample
URI: MIXS:0000427
"},{"location":"ammonium/#inheritance","title":"Inheritance","text":"name: ammonium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nmultivalued: false\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of ammonium nitrogen in the sample
URI: nmdc:ammonium_nitrogen
"},{"location":"ammonium_nitrogen/#inheritance","title":"Inheritance","text":"name: ammonium_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nis_a: attribute\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:amount_collected
"},{"location":"amount_collected/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity yes"},{"location":"amount_collected/#properties","title":"Properties","text":"name: amount_collected\ntitle: amount collected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: amount_collected\ndomain_of:\n- MaterialSamplingActivity\nrange: QuantityValue\ninlined: true\n\nThe unit of illuminance and luminous emittance, measuring luminous flux per unit area
URI: MIXS:0000140
"},{"location":"amount_light/#inheritance","title":"Inheritance","text":"name: amount_light\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nmultivalued: false\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:analysis_identifiers
"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: analysis_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSelect all the data types associated or available for this biosample
URI: nmdc:analysis_type
"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":"Range: AnalysisTypeEnum
Multivalued: True
Recommended: True
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; proteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nmultivalued: true\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: analysis_type_enum\nrecommended: true\n\nInformation about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)
URI: MIXS:0000247
"},{"location":"ances_data/#inheritance","title":"Inheritance","text":"name: ances_data\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about either pedigree or other ancestral information description\n (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nmultivalued: false\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000644
"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":"name: annual_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nmultivalued: false\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMean annual temperature
URI: MIXS:0000642
"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":"name: annual_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nmultivalued: false\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens
URI: MIXS:0000553
"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: antibiotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving antibiotic administration; should\n include the name of antibiotic, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nmultivalued: true\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAPI gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)
URI: MIXS:0000157
"},{"location":"api/#inheritance","title":"Inheritance","text":"name: api\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nmultivalued: false\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: prov:hadRole
"},{"location":"applied_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_role/#properties","title":"Properties","text":"name: applied_role\ndeprecated: A credit association may have multiple roles. So, use the applied roles\n slot.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nslot_uri: prov:hadRole\nalias: applied_role\ndomain_of:\n- CreditAssociation\nrange: credit enum\n\nURI: nmdc:applied_roles
"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":"Range: CreditEnum
Multivalued: True
Required: True
name: applied_roles\nannotations:\n display_hint:\n tag: display_hint\n value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nmultivalued: true\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: credit enum\nrequired: true\n\nURI: nmdc:applies_to_person
"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":"Range: PersonValue
Required: True
name: applies_to_person\ntodos:\n- prov:agent takes an Agent object. Is a person value an Agent? Also try to relate\n to principal investigator slot? could include OBI:0000103 principal investigator\n role... do we need to define the OBI prefix?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\nAn architectural structure is a human-made, free-standing, immobile outdoor construction
URI: MIXS:0000774
"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":"name: arch_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nmultivalued: false\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000133
"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":"name: aromatics_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nmultivalued: false\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nA score for comparing metagenomic assembly quality from same sample.
URI: nmdc:asm_score
"},{"location":"asm_score/#inheritance","title":"Inheritance","text":"name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000135
"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":"name: asphaltenes_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nmultivalued: false\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:assembly_identifiers
"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":"name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\nMeasurement of atmospheric data; can include multiple data
URI: MIXS:0001097
"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: atmospheric_data\nannotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nmultivalued: true\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\n\nA attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template
URI: nmdc:attribute
"},{"location":"attribute/#inheritance","title":"Inheritance","text":"name: attribute\ndescription: 'A attribute of a biosample. Examples: depth, habitat, material. For\n NMDC, attributes SHOULD be mapped to terms within a MIxS template'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field\n- property\n- template field\n- key\n- characteristic\nrank: 1000\nabstract: true\nalias: attribute\nrange: string\n\nThe average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000141
"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":"name: avg_dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nmultivalued: false\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDaily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.
URI: MIXS:0000775
"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":"name: avg_occup\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nmultivalued: false\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000142
"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":"name: avg_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nmultivalued: false\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOne or more DOIs that links a study, or similar entiry, to information about the funding authority.
URI: nmdc:award_dois
"},{"location":"award_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: award_dois\ndescription: One or more DOIs that links a study, or similar entiry, to information\n about the funding authority.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n description: award_dois link to to an award document. Should not be used to link\n to datasets or publications. For example, doi:10.15485/1577267 is not an award\n doi, but a dataset doi.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: award_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nBacterial production in the water column measured by isotope uptake
URI: MIXS:0000683
"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":"name: bac_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nmultivalued: false\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of bacterial respiration in the water column
URI: MIXS:0000684
"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":"name: bac_resp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nmultivalued: false\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of bacterial carbon production
URI: MIXS:0000173
"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":"name: bacteria_carb_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nmultivalued: false\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nForce per unit area exerted against a surface by the weight of air above that surface
URI: MIXS:0000096
"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":"name: barometric_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nmultivalued: false\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nName of the basin (e.g. Campos)
URI: MIXS:0000290
"},{"location":"basin/#inheritance","title":"Inheritance","text":"name: basin\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nmultivalued: false\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe number of bathrooms in the building
URI: MIXS:0000776
"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":"name: bathroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nmultivalued: false\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe number of bedrooms in the building
URI: MIXS:0000777
"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":"name: bedroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nmultivalued: false\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of benzene in the sample
URI: MIXS:0000153
"},{"location":"benzene/#inheritance","title":"Inheritance","text":"name: benzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nmultivalued: false\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nthe specific protein identifier most correctly associated with the peptide sequence
URI: nmdc:best_protein
"},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"best_protein/#properties","title":"Properties","text":"name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nURI: nmdc:bin_name
"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":"name: bin_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:bin_quality
"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":"name: bin_quality\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:binned_contig_num
"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":"name: binned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nAmount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
URI: MIXS:0000653
"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: biochem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n a body of water to break down organic material present in a given water sample at\n certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nmultivalued: false\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nList of biocides (commercial name of product and supplier) and date of administration
URI: MIXS:0001011
"},{"location":"biocide/#inheritance","title":"Inheritance","text":"name: biocide\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nmultivalued: false\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\n\nMethod of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
URI: MIXS:0000456
"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":"name: biocide_admin_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nmultivalued: false\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:biogas_retention_time
"},{"location":"biogas_retention_time/#properties","title":"Properties","text":"name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\nURI: nmdc:biogas_temperature
"},{"location":"biogas_temperature/#properties","title":"Properties","text":"name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\nThe level of genome modification.
URI: MIXS:0000858
"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":"name: biol_stat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nmultivalued: false\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\n\nAmount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
URI: MIXS:0000174
"},{"location":"biomass/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: biomass\nannotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nmultivalued: true\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:biomaterial_purity
"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":"name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\nURI: nmdc:biosample_categories
"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":"Range: BiosampleCategoryEnum
Multivalued: True
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\n\nURI: nmdc:biosample_identifiers
"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: biosample_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of samples within it.
URI: nmdc:biosample_set
"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":"Range: Biosample
Multivalued: True
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\ninlined: true\ninlined_as_list: true\n\nInformation about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.
URI: MIXS:0001038
"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":"name: biotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nmultivalued: false\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nDescription of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
URI: MIXS:0000028
"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":"name: biotic_relationship\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n Y. The target organism is the subject of the relationship, and the other organism(s)\n is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nmultivalued: false\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\n\nConcentration of bishomohopanol
URI: MIXS:0000175
"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":"name: bishomohopanol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nmultivalued: false\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nResting diastolic blood pressure, measured as mm mercury
URI: MIXS:0000258
"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":"name: blood_press_diast\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nmultivalued: false\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nResting systolic blood pressure, measured as mm mercury
URI: MIXS:0000259
"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":"name: blood_press_syst\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nmultivalued: false\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of bromide
URI: MIXS:0000176
"},{"location":"bromide/#inheritance","title":"Inheritance","text":"name: bromide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nmultivalued: false\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building design, construction and operation documents
URI: MIXS:0000787
"},{"location":"build_docs/#inheritance","title":"Inheritance","text":"name: build_docs\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nmultivalued: false\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\n\nThe primary function for which a building or discrete part of a building is intended to be used
URI: MIXS:0000761
"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":"Range: BuildOccupTypeEnum
Multivalued: True
name: build_occup_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The primary function for which a building or discrete part of a building\n is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nmultivalued: true\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\n\nA location (geography) where a building is set
URI: MIXS:0000768
"},{"location":"building_setting/#inheritance","title":"Inheritance","text":"name: building_setting\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nmultivalued: false\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\n\nThe age of the built structure since construction
URI: MIXS:0000145
"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":"name: built_struc_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nmultivalued: false\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe characterization of the location of the built structure as high or low human density
URI: MIXS:0000778
"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":"name: built_struc_set\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The characterization of the location of the built structure as high or\n low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nmultivalued: false\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\n\nA physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
URI: MIXS:0000721
"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":"name: built_struc_type\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nmultivalued: false\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of calcium in the sample
URI: MIXS:0000432
"},{"location":"calcium/#inheritance","title":"Inheritance","text":"name: calcium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nmultivalued: false\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\na slot that can be added and removed as evidence that schema changes have propagated to other systems
URI: nmdc:canary
"},{"location":"canary/#properties","title":"Properties","text":"name: canary\ndescription: a slot that can be added and removed as evidence that schema changes\n have propagated to other systems\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: canary\nrange: string\n\nCarbon dioxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000097
"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":"name: carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nmultivalued: false\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCarbon monoxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000098
"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":"name: carb_monoxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nmultivalued: false\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nRatio of amount or concentrations of carbon to nitrogen
URI: MIXS:0000310
"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":"name: carb_nitro_ratio\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nmultivalued: false\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe area of the ceiling space within the room
URI: MIXS:0000148
"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":"name: ceil_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nmultivalued: false\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000779
"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":"name: ceil_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nmultivalued: false\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\n\nThe type of material used to finish a ceiling
URI: MIXS:0000780
"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":"name: ceil_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nmultivalued: false\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\n\nThe construction format of the ceiling
URI: MIXS:0000782
"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":"name: ceil_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nmultivalued: false\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe feel, appearance, or consistency of a ceiling surface
URI: MIXS:0000783
"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":"name: ceil_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nmultivalued: false\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\n\nThe ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
URI: MIXS:0000143
"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":"name: ceil_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n Generally this means concrete that is exposed. A metal deck that supports a concrete\n slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nmultivalued: false\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of ceiling according to the ceiling's appearance or construction
URI: MIXS:0000784
"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":"name: ceil_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nmultivalued: false\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\n\nSigns of the presence of mold or mildew on the ceiling
URI: MIXS:0000781
"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":"name: ceil_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nmultivalued: false\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
URI: MIXS:0000751
"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":"Range: ControlledTermValue
Multivalued: True
name: chem_administration\nannotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nmultivalued: true\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nTreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens
URI: MIXS:0000555
"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: chem_mutagen\nannotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nmultivalued: true\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\n\nA measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite
URI: MIXS:0000656
"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: chem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nmultivalued: false\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)
URI: MIXS:0000457
"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":"name: chem_treat_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nmultivalued: false\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\n\nList of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included
URI: MIXS:0001012
"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":"name: chem_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the product\n and name of the supplier should be provided. The date of administration should also\n be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nmultivalued: false\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nfrom reaction participant class
URI: nmdc:chemical
"},{"location":"chemical/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionParticipant Instances of this link a reaction to a chemical entity participant no"},{"location":"chemical/#properties","title":"Properties","text":"name: chemical\ndescription: from reaction participant class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical\ndomain_of:\n- ReactionParticipant\nrange: ChemicalEntity\n\nA generic grouping for molecular formulae and empirical formulae
URI: nmdc:chemical_formula
"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":"name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\nTool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.
URI: MIXS:0000052
"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":"name: chimera_check\nannotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nmultivalued: false\nalias: chimera_check\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nConcentration of chloride in the sample
URI: MIXS:0000429
"},{"location":"chloride/#inheritance","title":"Inheritance","text":"name: chloride\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nmultivalued: false\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of chlorophyll
URI: MIXS:0000177
"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":"name: chlorophyll\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nmultivalued: false\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTreatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
URI: MIXS:0001040
"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: climate_environment\nannotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nmultivalued: true\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe Site from which a Biosample was collected
URI: nmdc:collected_from
"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collected_from/#properties","title":"Properties","text":"name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Biosample\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\nURI: nmdc:collected_into
"},{"location":"collected_into/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity yes"},{"location":"collected_into/#properties","title":"Properties","text":"name: collected_into\ntitle: collected into\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_into\ndomain_of:\n- MaterialSamplingActivity\nrange: MaterialContainer\ninlined: true\n\nURI: nmdc:collecting_biosamples_from_site_set
"},{"location":"collecting_biosamples_from_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"collecting_biosamples_from_site_set/#properties","title":"Properties","text":"Range: CollectingBiosamplesFromSite
Multivalued: True
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Database\nmultivalued: true\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\ninlined: true\ninlined_as_list: true\n\nThe time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
URI: MIXS:0000011
"},{"location":"collection_date/#inheritance","title":"Inheritance","text":"name: collection_date\nannotations:\n expected_value:\n tag: expected_value\n value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n interval. In case no exact time is available, the date/time can be right truncated\n i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nmultivalued: false\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nDate the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_date_inc
"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe time of sampling, either as an instance (single point) or interval.
URI: nmdc:collection_time
"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_time_inc
"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:community
"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":"name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:completeness
"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"completeness/#properties","title":"Properties","text":"name: completeness\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- MagBin\nrange: float\n\nURI: nmdc:completion_date
"},{"location":"completion_date/#properties","title":"Properties","text":"name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\nIf provided, specifies the compression type
URI: nmdc:compression_type
"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":"name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\nElectrical conductivity of water
URI: MIXS:0000692
"},{"location":"conduc/#inheritance","title":"Inheritance","text":"name: conduc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nmultivalued: false\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:container_size
"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialContainer no"},{"location":"container_size/#properties","title":"Properties","text":"name: container_size\ntitle: container size\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: container_size\ndomain_of:\n- MaterialContainer\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:container_type
"},{"location":"container_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialContainer no"},{"location":"container_type/#properties","title":"Properties","text":"name: container_type\ntitle: container type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: container_type\ndomain_of:\n- MaterialContainer\nrange: ContainerTypeEnum\n\nURI: nmdc:contamination
"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"contamination/#properties","title":"Properties","text":"name: contamination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- MagBin\nrange: float\n\nTotal size in bp of all contigs.
URI: nmdc:contig_bp
"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":"name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase
URI: nmdc:contigs
"},{"location":"contigs/#inheritance","title":"Inheritance","text":"name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe cooling system identifier
URI: MIXS:0000785
"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":"name: cool_syst_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nmultivalued: false\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nbasic fields
URI: nmdc:core_field
"},{"location":"core_field/#inheritance","title":"Inheritance","text":"name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:count
"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"count/#properties","title":"Properties","text":"name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\n\nthis project was made using the LinkML framework
"},{"location":"crop_rotation/","title":"Slot: crop_rotation","text":"Whether or not crop is rotated, and if yes, rotation schedule
URI: MIXS:0000318
"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":"name: crop_rotation\nannotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nmultivalued: false\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\n\nGiven a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
URI: nmdc:ctg_l50
"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":"name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
URI: nmdc:ctg_l90
"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":"name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all contigs of that length or longer contains\n at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_logsum
"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":"name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_max
"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":"name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.
URI: nmdc:ctg_n50
"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":"name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
URI: nmdc:ctg_n90
"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":"name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:ctg_powsum
"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":"name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nName or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.
URI: MIXS:0001041
"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":"name: cult_root_med\nannotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n can be the name of a commonly used medium or reference to a specific medium, e.g.\n Murashige and Skoog medium. If the medium has not been formally published, use the\n rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nmultivalued: false\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\n\nPresent state of sample site
URI: MIXS:0001080
"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":"name: cur_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nmultivalued: false\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\n\nVegetation classification from one or more standard classification systems, or agricultural crop
URI: MIXS:0000312
"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":"name: cur_vegetation\nannotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nmultivalued: false\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in vegetation classification
URI: MIXS:0000314
"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":"name: cur_vegetation_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nmultivalued: false\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of data objects within it.
URI: nmdc:data_object_set
"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":"Range: DataObject
Multivalued: True
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\ninlined: true\ninlined_as_list: true\n\nThe type of file represented by the data object.
URI: nmdc:data_object_type
"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":"name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: file type enum\n\nOne or more DOIs that links a study, or similar entity, to the generated data.
URI: nmdc:dataset_dois
"},{"location":"dataset_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: dataset_dois\ndescription: One or more DOIs that links a study, or similar entity, to the generated\n data.\nexamples:\n- value: doi:10.15485/1577267\n description: dataset_dois link to data encoded in a defined structure (as defined\n by DataCite). Should not be used to link to publications or administrative information\n like funding requests or awards.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: dataset_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nfrom database class
URI: nmdc:date_created
"},{"location":"date_created/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data yes"},{"location":"date_created/#properties","title":"Properties","text":"name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\ndomain_of:\n- Database\nrange: string\n\nThe date of the last time it rained
URI: MIXS:0000786
"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":"name: date_last_rain\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nmultivalued: false\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nDensity of the sample, which is its mass per unit volume (aka volumetric mass density)
URI: MIXS:0000435
"},{"location":"density/#inheritance","title":"Inheritance","text":"name: density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nmultivalued: false\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMain depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000992
"},{"location":"depos_env/#inheritance","title":"Inheritance","text":"name: depos_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nmultivalued: false\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\n\nThe vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
URI: MIXS:0000018
"},{"location":"depth/#inheritance","title":"Inheritance","text":"name: depth\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth can\n be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nmultivalued: false\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\na human-readable description of a thing
URI: dcterms:description
"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes NamedThing a databased entity or concept/class no ImageValue An attribute value representing an image no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CollectingBiosamplesFromSite no DataObject An object that primarily consists of symbols that represent information yes Biosample Biological source material which can be characterized by an experiment no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no MaterialEntity no ProcessedSample no AnalyticalSample no Site no PlannedProcess no OntologyClass no EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"description/#properties","title":"Properties","text":"name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- Study\n- NamedThing\n- ImageValue\nrange: string\n\nURI: nmdc:device_type
"},{"location":"device_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"device_type/#properties","title":"Properties","text":"name: device_type\ntitle: device type\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker type\nrank: 1000\nalias: device_type\ndomain_of:\n- LabDevice\nrange: DeviceTypeEnum\n\nThe temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
URI: MIXS:0000129
"},{"location":"dew_point/#inheritance","title":"Inheritance","text":"name: dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nmultivalued: false\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of diether lipids; can include multiple types of diether lipids
URI: MIXS:0000178
"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: diether_lipids\nannotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nmultivalued: true\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\n\nOne of l->r, r->l, bidirectional, neutral
URI: nmdc:direction
"},{"location":"direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"direction/#properties","title":"Properties","text":"name: direction\ndescription: One of l->r, r->l, bidirectional, neutral\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: direction\ndomain_of:\n- Reaction\nrange: string\n\nWhen rendering information, this attribute to specify the order in which the information should be rendered.
URI: nmdc:display_order
"},{"location":"display_order/#inheritance","title":"Inheritance","text":"name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: display_order\ndomain_of:\n- ImageValue\nrange: string\n\nConcentration of dissolved carbon dioxide in the sample or liquid portion of the sample
URI: MIXS:0000436
"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":"name: diss_carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nmultivalued: false\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved hydrogen
URI: MIXS:0000179
"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":"name: diss_hydrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nmultivalued: false\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
URI: MIXS:0000434
"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":"name: diss_inorg_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nmultivalued: false\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved inorganic nitrogen
URI: MIXS:0000698
"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":"name: diss_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nmultivalued: false\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved inorganic phosphorus in the sample
URI: MIXS:0000106
"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":"name: diss_inorg_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nmultivalued: false\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved iron in the sample
URI: MIXS:0000139
"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":"name: diss_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nmultivalued: false\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
URI: MIXS:0000433
"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":"name: diss_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nmultivalued: false\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
URI: MIXS:0000162
"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":"name: diss_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nmultivalued: false\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved oxygen
URI: MIXS:0000119
"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":"name: diss_oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nmultivalued: false\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
URI: MIXS:0000438
"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":"name: diss_oxygen_fluid\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nmultivalued: false\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:dissolution_aided_by
"},{"location":"dissolution_aided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_aided_by/#properties","title":"Properties","text":"name: dissolution_aided_by\ntitle: dissolution aided by\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker\nrank: 1000\nalias: dissolution_aided_by\ndomain_of:\n- DissolvingActivity\nrange: LabDevice\ninlined: true\n\nURI: nmdc:dissolution_reagent
"},{"location":"dissolution_reagent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_reagent/#properties","title":"Properties","text":"name: dissolution_reagent\ntitle: dissolution reagent\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solvent\nrank: 1000\nalias: dissolution_reagent\ndomain_of:\n- DissolvingActivity\nrange: SolventEnum\n\nURI: nmdc:dissolution_volume
"},{"location":"dissolution_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_volume/#properties","title":"Properties","text":"name: dissolution_volume\ntitle: dissolution volume\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volume\nrank: 1000\nalias: dissolution_volume\ndomain_of:\n- DissolvingActivity\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:dissolved_in
"},{"location":"dissolved_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolved_in/#properties","title":"Properties","text":"name: dissolved_in\ntitle: dissolved in\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- container\nrank: 1000\nalias: dissolved_in\ndomain_of:\n- DissolvingActivity\nrange: MaterialContainer\ninlined: true\n\nURI: nmdc:dissolving_activity_set
"},{"location":"dissolving_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"dissolving_activity_set/#properties","title":"Properties","text":"Range: DissolvingActivity
Multivalued: True
name: dissolving_activity_set\ntitle: dissolving activity set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: dissolving_activity_set\ndomain_of:\n- Database\nrange: DissolvingActivity\ninlined: true\ninlined_as_list: true\n\n260/280 measurement of DNA sample purity
URI: nmdc:dna_absorb1
"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n260/230 measurement of DNA sample purity
URI: nmdc:dna_absorb2
"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\nProvide information on the site your DNA sample was collected from
URI: nmdc:dna_collect_site
"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_concentration
"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nTube or plate (96-well)
URI: nmdc:dna_cont_type
"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:dna_cont_well
"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:dna_container_id
"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_dnase
"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:dna_isolate_meth
"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:dna_organisms
"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_project_contact
"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_samp_id
"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will be\n prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nSolution in which the DNA sample has been suspended
URI: nmdc:dna_sample_format
"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":"Range: DnaSampleFormatEnum
Recommended: True
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: dna_sample_format_enum\nrecommended: true\n\nGive the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:dna_sample_name
"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project
"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_name
"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_pi
"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_volume
"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nURI: nmdc:dnase_rna
"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\nA digital object identifier, which is intended to persistantly identify some resource on the web.
URI: nmdc:dois
"},{"location":"dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: dois\ndescription: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\ntodos:\n- the previous doi slot was an attribute, but attribute seems committed to biosamples\n- should we assert a parent term here?\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite pdf, on pp48-53 as\n of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\naliases:\n- DOIs\n- digital object identifiers\nrank: 1000\nabstract: true\nmultivalued: true\nalias: dois\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe composite type of the door
URI: MIXS:0000795
"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":"name: door_comp_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nmultivalued: false\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\n\nThe phsical condition of the door
URI: MIXS:0000788
"},{"location":"door_cond/#inheritance","title":"Inheritance","text":"name: door_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nmultivalued: false\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\n\nThe direction the door opens
URI: MIXS:0000789
"},{"location":"door_direct/#inheritance","title":"Inheritance","text":"name: door_direct\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nmultivalued: false\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\n\nThe relative location of the door in the room
URI: MIXS:0000790
"},{"location":"door_loc/#inheritance","title":"Inheritance","text":"name: door_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nmultivalued: false\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\n\nThe material the door is composed of
URI: MIXS:0000791
"},{"location":"door_mat/#inheritance","title":"Inheritance","text":"name: door_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nmultivalued: false\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\n\nThe type of movement of the door
URI: MIXS:0000792
"},{"location":"door_move/#inheritance","title":"Inheritance","text":"name: door_move\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nmultivalued: false\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\n\nThe size of the door
URI: MIXS:0000158
"},{"location":"door_size/#inheritance","title":"Inheritance","text":"name: door_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nmultivalued: false\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of door material
URI: MIXS:0000794
"},{"location":"door_type/#inheritance","title":"Inheritance","text":"name: door_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nmultivalued: false\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\n\nThe type of metal door
URI: MIXS:0000796
"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":"name: door_type_metal\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nmultivalued: false\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\n\nThe type of wood door
URI: MIXS:0000797
"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":"name: door_type_wood\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nmultivalued: false\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\n\nSigns of the presence of mold or mildew on a door
URI: MIXS:0000793
"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":"name: door_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nmultivalued: false\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nVisible waveband radiance and irradiance measurements in the water column
URI: MIXS:0000703
"},{"location":"down_par/#inheritance","title":"Inheritance","text":"name: down_par\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square centimeter\n per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nmultivalued: false\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDrainage classification from a standard system such as the USDA system
URI: MIXS:0001085
"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":"name: drainage_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nmultivalued: false\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\n\nThe buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
URI: MIXS:0000798
"},{"location":"drawings/#inheritance","title":"Inheritance","text":"name: drawings\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nmultivalued: false\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\n\nAn ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.
URI: nmdc:ecosystem
"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":"name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n and all the organisms (biotic factors) that interact with this environment. Ecosystem\n is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism or environmental\n sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n and Engineered. They represent samples collected from a natural environment or from\n another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.
URI: nmdc:ecosystem_category
"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":"name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n specific characteristics of the environment from where an organism or sample is\n isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or phyla\n and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nA unique id representing the GOLD classifiers associated with a sample.
URI: nmdc:ecosystem_path_id
"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":"name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\nEcosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.
URI: nmdc:ecosystem_subtype
"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":"name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.
URI: nmdc:ecosystem_type
"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":"name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still broad\n but specific to the characteristics of a given environment. Ecosystem type is in\n position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nPercentage of volatile solids removed from the anaerobic digestor
URI: MIXS:0000657
"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":"name: efficiency_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nmultivalued: false\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nElevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.
URI: MIXS:0000093
"},{"location":"elev/#inheritance","title":"Inheritance","text":"name: elev\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the surface,\n such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nmultivalued: false\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: QuantityValue\n\nThe number of elevators within the built structure
URI: MIXS:0000799
"},{"location":"elevator/#inheritance","title":"Inheritance","text":"name: elevator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nmultivalued: false\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\n\nAn email address for an entity such as a person. This should be the primary email address used.
URI: schema:email
"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":"name: email\ndescription: An email address for an entity such as a person. This should be the primary\n email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\nIf true, the data are embargoed and not available for public access.
URI: nmdc:embargoed
"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":"Range: Boolean
Recommended: True
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may nto be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\nA list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.
URI: nmdc:emsl_biosample_identifiers
"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nmultivalued: true\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:emsl_identifiers
"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_dois One or more DOIs that links to an EMSL Research Campaign page None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\nOne or more DOIs that links to an EMSL Research Campaign page.
URI: nmdc:emsl_project_dois
"},{"location":"emsl_project_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: emsl_project_dois\ndescription: One or more DOIs that links to an EMSL Research Campaign page.\ntitle: EMSL Project DOI\ntodos:\n- Make as a subproperty of award_dois\nexamples:\n- value: doi:10.46936/intm.proj.2021.6014\n description: emsl_project_dois link to the document outlining the EMSL specific\n award for the project. Should not be used to link to datasets or publications.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmixins:\n- emsl_identifiers\nmultivalued: true\nalias: emsl_project_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe temperature at which the sample should be stored upon delivery to EMSL
URI: nmdc:emsl_store_temp
"},{"location":"emsl_store_temp/#properties","title":"Properties","text":"Range: String
Recommended: True
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\nAmount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
URI: MIXS:0000660
"},{"location":"emulsions/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: emulsions\nannotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nmultivalued: true\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA
URI: nmdc:encodes
"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":"name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n a CDS feature or gene feature which will encode a protein. It can also be used by\n a nc transcript ot gene feature that encoded a ncRNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\nThe end of the feature in positive 1-based integer coordinates
URI: nmdc:end
"},{"location":"end/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was ended
URI: nmdc:end_date
"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PlannedProcess no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"end_date/#properties","title":"Properties","text":"name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nURI: nmdc:ended_at_time
"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"ended_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- Activity\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nReport the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
URI: MIXS:0000012
"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":"name: env_broad_scale\nannotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n or more pipes.\ndescription: 'Report the major environmental system the sample or specimen came from.\n The system(s) identified should have a coarse spatial grain, to provide the general\n environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample\n from the photic zone in middle of the Atlantic Ocean\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nmultivalued: false\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nReport the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
URI: MIXS:0000013
"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":"name: env_local_scale\nannotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at time\n of sampling.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various\n vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer\n [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer\n [ENVO:01000336].'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nmultivalued: false\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nReport the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
URI: MIXS:0000014
"},{"location":"env_medium/#inheritance","title":"Inheritance","text":"name: env_medium\nannotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend subclasses\n of environmental material [ENVO:00010483].\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n or specimen at the time of sampling. We recommend using subclasses of ''environmental\n material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the\n Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck\n on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nmultivalued: false\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nMIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
URI: nmdc:env_package
"},{"location":"env_package/#inheritance","title":"Inheritance","text":"name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the name\n of the environmental package, a selection of fields can be made from the subtables\n and can be reported\nin_subset:\n- mixs extension\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nis_a: attribute\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\nfield describing environmental aspect of a sample
URI: nmdc:environment_field
"},{"location":"environment_field/#inheritance","title":"Inheritance","text":"name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\nThe number of escalators within the built structure
URI: MIXS:0000800
"},{"location":"escalator/#inheritance","title":"Inheritance","text":"name: escalator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nmultivalued: false\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of ESS-DIVE dataset DOIs
URI: nmdc:ess_dive_datasets
"},{"location":"ess_dive_datasets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ess_dive_datasets/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: ess_dive_datasets\ndescription: List of ESS-DIVE dataset DOIs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: ess_dive_datasets\ndomain_of:\n- Study\nrange: string\n\nConcentration of ethylbenzene in the sample
URI: MIXS:0000155
"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":"name: ethylbenzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nmultivalued: false\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nfrom database class
URI: nmdc:etl_software_version
"},{"location":"etl_software_version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data yes"},{"location":"etl_software_version/#properties","title":"Properties","text":"name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\ndomain_of:\n- Database\nrange: string\n\nURI: nmdc:execution_resource
"},{"location":"execution_resource/#inheritance","title":"Inheritance","text":"name: execution_resource\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: execution_resource\ndomain_of:\n- WorkflowExecutionActivity\nrange: string\n\nThe amount of exposed ductwork in the room
URI: MIXS:0000144
"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":"name: exp_duct\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nmultivalued: false\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of exposed pipes in the room
URI: MIXS:0000220
"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":"name: exp_pipe\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nmultivalued: false\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nExperimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
URI: MIXS:0000008
"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":"name: experimental_factor\nannotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in an\n increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nmultivalued: false\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nOther details about your sample that you feel can't be accurately represented in the available columns.
URI: nmdc:experimental_factor_other
"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":"Range: String
Recommended: True
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe number of exterior doors in the built structure
URI: MIXS:0000170
"},{"location":"ext_door/#inheritance","title":"Inheritance","text":"name: ext_door\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nmultivalued: false\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe orientation of the exterior wall
URI: MIXS:0000817
"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":"name: ext_wall_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nmultivalued: false\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\n\nThe compass direction the exterior window of the room is facing
URI: MIXS:0000818
"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":"name: ext_window_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nmultivalued: false\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\n\nLink to corresponding identifier in external database
URI: nmdc:external_database_identifiers
"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nmultivalued: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:extraction_method
"},{"location":"extraction_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_method/#properties","title":"Properties","text":"name: extraction_method\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: extraction_method\ndomain_of:\n- Extraction\nrange: string\n\nThis property links a database object to the set of extractions within it.
URI: nmdc:extraction_set
"},{"location":"extraction_set/#inheritance","title":"Inheritance","text":"Range: Extraction
Multivalued: True
name: extraction_set\ndescription: This property links a database object to the set of extractions within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: extraction_set\ndomain_of:\n- Database\nrange: Extraction\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:extraction_target
"},{"location":"extraction_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_target/#properties","title":"Properties","text":"name: extraction_target\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: extraction_target\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\n\nUnusual physical events that may have affected microbial populations
URI: MIXS:0000320
"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":"name: extreme_event\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nmultivalued: false\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nSoil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
URI: MIXS:0001083
"},{"location":"fao_class/#inheritance","title":"Inheritance","text":"name: fao_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nmultivalued: false\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\n\nTODO: Yuri to write
URI: nmdc:feature_type
"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":"name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\nInformation about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens
URI: MIXS:0000556
"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fertilizer_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nmultivalued: true\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nName of the hydrocarbon field (e.g. Albacora)
URI: MIXS:0000291
"},{"location":"field/#inheritance","title":"Inheritance","text":"name: field\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nmultivalued: false\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:field_research_site_set
"},{"location":"field_research_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"field_research_site_set/#properties","title":"Properties","text":"Range: FieldResearchSite
Multivalued: True
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Database\nmultivalued: true\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\ninlined: true\ninlined_as_list: true\n\nSize of the file in bytes
URI: nmdc:file_size_bytes
"},{"location":"file_size_bytes/#inheritance","title":"Inheritance","text":"name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\nType of filter used or how the sample was filtered
URI: nmdc:filter_method
"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":"Range: String
Recommended: True
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nA device which removes solid particulates or airborne molecular contaminants
URI: MIXS:0000765
"},{"location":"filter_type/#inheritance","title":"Inheritance","text":"Range: FilterTypeEnum
Multivalued: True
name: filter_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nmultivalued: true\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\n\nHistorical and/or physical evidence of fire
URI: MIXS:0001086
"},{"location":"fire/#inheritance","title":"Inheritance","text":"name: fire\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nmultivalued: false\nalias: fire\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nA firebox with chimney
URI: MIXS:0000802
"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":"name: fireplace_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nmultivalued: false\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nHistorical and/or physical evidence of flooding
URI: MIXS:0000319
"},{"location":"flooding/#inheritance","title":"Inheritance","text":"name: flooding\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nmultivalued: false\nalias: flooding\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nThe time period since installment of the carpet or flooring
URI: MIXS:0000164
"},{"location":"floor_age/#inheritance","title":"Inheritance","text":"name: floor_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nmultivalued: false\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe area of the floor space within the room
URI: MIXS:0000165
"},{"location":"floor_area/#inheritance","title":"Inheritance","text":"name: floor_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nmultivalued: false\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000803
"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":"name: floor_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nmultivalued: false\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\n\nThe number of floors in the building, including basements and mechanical penthouse
URI: MIXS:0000225
"},{"location":"floor_count/#inheritance","title":"Inheritance","text":"name: floor_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nmultivalued: false\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe floor covering type; the finished surface that is walked on
URI: MIXS:0000804
"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":"name: floor_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nmultivalued: false\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\n\nRefers to the structural elements and subfloor upon which the finish flooring is installed
URI: MIXS:0000806
"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":"name: floor_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nmultivalued: false\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\n\nThe ability of the floor to provide inertia against temperature fluctuations
URI: MIXS:0000166
"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":"name: floor_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nmultivalued: false\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSigns of the presence of mold or mildew in a room
URI: MIXS:0000805
"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":"name: floor_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nmultivalued: false\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\n\nRaw or converted fluorescence of water
URI: MIXS:0000704
"},{"location":"fluor/#inheritance","title":"Inheritance","text":"name: fluor\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nmultivalued: false\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
URI: MIXS:0000226
"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":"name: freq_clean\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nmultivalued: false\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of times a meal is cooked per week
URI: MIXS:0000227
"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":"name: freq_cook\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nmultivalued: false\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:functional_annotation_agg
"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":"Range: FunctionalAnnotationAggMember
Multivalued: True
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of all functional annotations
URI: nmdc:functional_annotation_set
"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":"Range: FunctionalAnnotation
Multivalued: True
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\ninlined: true\ninlined_as_list: true\n\nA list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.
URI: nmdc:funding_sources
"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process applications\n and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nmultivalued: true\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\n\nInformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens
URI: MIXS:0000557
"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fungicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nmultivalued: true\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe types of furniture present in the sampled room
URI: MIXS:0000807
"},{"location":"furniture/#inheritance","title":"Inheritance","text":"name: furniture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nmultivalued: false\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\n\nThe gap size percentage of all scaffolds.
URI: nmdc:gap_pct
"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":"name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nUse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
URI: MIXS:0000558
"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_environment\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nmultivalued: true\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nAmount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
URI: MIXS:0000661
"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_substances\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nmultivalued: true\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\n\nAverage of GC content of all contigs.
URI: nmdc:gc_avg
"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":"name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nStandard deviation of GC content of all contigs.
URI: nmdc:gc_std
"},{"location":"gc_std/#inheritance","title":"Inheritance","text":"name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe gender type of the restroom
URI: MIXS:0000808
"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":"name: gender_restroom\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nmultivalued: false\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\n\nURI: nmdc:gene_count
"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":"name: gene_count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:gene_function_id
"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":"name: gene_function_id\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\n\nGenetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection
URI: MIXS:0000859
"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":"name: genetic_mod\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nmultivalued: false\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of all features
URI: nmdc:genome_feature_set
"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":"Range: GenomeFeature
Multivalued: True
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\ninlined: true\ninlined_as_list: true\n\nThe geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)
URI: MIXS:0000010
"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":"name: geo_loc_name\nannotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n name followed by specific region name. Country or sea names should be chosen from\n the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nmultivalued: false\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nA positive 1-based integer coordinate indicating start or end
URI: nmdc:gff_coordinate
"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n plasmids, and some viral genomes), the requirement for start to be less than or\n equal to end is satisfied by making end = the position of the end + the length of\n the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\nURI: nmdc:git_url
"},{"location":"git_url/#inheritance","title":"Inheritance","text":"name: git_url\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: git_url\ndomain_of:\n- WorkflowExecutionActivity\nrange: string\n\nMeasurement of glucosidase activity
URI: MIXS:0000137
"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":"name: glucosidase_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nmultivalued: false\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:gnps_identifiers
"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\nidentifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results
URI: nmdc:gnps_task_identifiers
"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gnps\\.task:[a-f0-9]+$
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nmultivalued: true\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^gnps\\.task:[a-f0-9]+$\n\nidentifiers for corresponding analysis project in GOLD
URI: nmdc:gold_analysis_project_identifiers
"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Ga[0-9]+$
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotationActivity\n- MetatranscriptomeAnnotationActivity\nrange: external_identifier\npattern: ^gold:Ga[0-9]+$\n\nidentifiers for corresponding sample in GOLD
URI: nmdc:gold_biosample_identifiers
"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gb[0-9]+$
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^gold:Gb[0-9]+$\n\nURI: nmdc:gold_identifiers
"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD None Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None OmicsProcessing gold_analysis_project_identifiers identifiers for corresponding analysis project in GOLD None MetagenomeAnnotationActivity, MetatranscriptomeAnnotationActivity"},{"location":"gold_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\nThis is a grouping for any of the gold path fields
URI: nmdc:gold_path_field
"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":"name: gold_path_field\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nabstract: true\nalias: gold_path_field\nrange: string\n\nidentifiers for corresponding sequencing project in GOLD
URI: nmdc:gold_sequencing_project_identifiers
"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gp[0-9]+$
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- OmicsProcessing\nrange: external_identifier\npattern: ^gold:Gp[0-9]+$\n\nidentifiers for corresponding project(s) in GOLD
URI: nmdc:gold_study_identifiers
"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gs[0-9]+$
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^gold:Gs[0-9]+$\n\nWhether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
URI: MIXS:0000875
"},{"location":"gravidity/#inheritance","title":"Inheritance","text":"name: gravidity\nannotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nmultivalued: false\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments
URI: MIXS:0000559
"},{"location":"gravity/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gravity\nannotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nmultivalued: true\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research
URI: MIXS:0001043
"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":"name: growth_facil\nannotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nmultivalued: false\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nCharacteristic shape, appearance or growth form of a plant species
URI: MIXS:0001044
"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":"name: growth_habit\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nmultivalued: false\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\n\nInformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens
URI: MIXS:0000560
"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: growth_hormone_regm\nannotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple growth hormone\n regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nmultivalued: true\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:gtdbtk_class
"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":"name: gtdbtk_class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_domain
"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":"name: gtdbtk_domain\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_family
"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":"name: gtdbtk_family\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_genus
"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":"name: gtdbtk_genus\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_order
"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":"name: gtdbtk_order\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_phylum
"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":"name: gtdbtk_phylum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_species
"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":"name: gtdbtk_species\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:habitat
"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"habitat/#properties","title":"Properties","text":"name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\nThe total count of hallways and cooridors in the built structure
URI: MIXS:0000228
"},{"location":"hall_count/#inheritance","title":"Inheritance","text":"name: hall_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nmultivalued: false\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe handidness of the individual sampled
URI: MIXS:0000809
"},{"location":"handidness/#inheritance","title":"Inheritance","text":"name: handidness\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nmultivalued: false\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\n\nLinks a quantity value to a boolean
URI: nmdc:has_boolean_value
"},{"location":"has_boolean_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BooleanValue A value that is a boolean no"},{"location":"has_boolean_value/#properties","title":"Properties","text":"name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: false\nalias: has_boolean_value\ndomain_of:\n- BooleanValue\nrange: boolean\n\nA reference to a file that holds calibration information.
URI: nmdc:has_calibration
"},{"location":"has_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_calibration/#properties","title":"Properties","text":"name: has_calibration\ndescription: A reference to a file that holds calibration information.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_calibration\ndomain_of:\n- MetabolomicsAnalysisActivity\n- NomAnalysisActivity\nrange: string\n\nThis slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study
URI: prov:qualifiedAssociation
"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":"Range: CreditAssociation
Multivalued: True
name: has_credit_associations\nannotations:\n display_hint:\n tag: display_hint\n value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\nnotes:\n- 'had just been \"inlined: true\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Study\nslot_uri: prov:qualifiedAssociation\nmultivalued: true\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_function
"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":"Range: String
Regex pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\nAn input to a process.
URI: nmdc:has_input
"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes PlannedProcess no Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes CollectingBiosamplesFromSite yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_input/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\ndomain: NamedThing\nmultivalued: true\nalias: has_input\ndomain_of:\n- BiosampleProcessing\n- OmicsProcessing\n- WorkflowExecutionActivity\n- PlannedProcess\nrange: NamedThing\n\nThe maximum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_maximum_numeric_value
"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: float\n\nURI: nmdc:has_metabolite_quantifications
"},{"location":"has_metabolite_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysisActivity no"},{"location":"has_metabolite_quantifications/#properties","title":"Properties","text":"Range: MetaboliteQuantification
Multivalued: True
name: has_metabolite_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_metabolite_quantifications\ndomain_of:\n- MetabolomicsAnalysisActivity\nrange: MetaboliteQuantification\n\nThe minimum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_minimum_numeric_value
"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: float\n\nURI: nmdc:has_numeric_value
"},{"location":"has_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_numeric_value/#properties","title":"Properties","text":"name: has numeric value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_numeric_value\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: double\n\nAn output biosample to a processing step
URI: nmdc:has_output
"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes PlannedProcess no Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes CollectingBiosamplesFromSite yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_output/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_output\ndescription: An output biosample to a processing step\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\ndomain: NamedThing\nmultivalued: true\nalias: has_output\ndomain_of:\n- OmicsProcessing\n- WorkflowExecutionActivity\n- PlannedProcess\nrange: NamedThing\n\nA pathway can be broken down to a series of reaction step
URI: nmdc:has_part
"},{"location":"has_part/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no"},{"location":"has_part/#properties","title":"Properties","text":"Range: Reaction
Multivalued: True
name: has_part\ndescription: A pathway can be broken down to a series of reaction step\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_part\ndomain_of:\n- Pathway\nrange: Reaction\n\nURI: nmdc:has_participants
"},{"location":"has_participants/#inheritance","title":"Inheritance","text":"name: has_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- RO:0000057\nrank: 1000\nabstract: true\nalias: has_participants\nrange: string\n\nURI: nmdc:has_peptide_quantifications
"},{"location":"has_peptide_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysisActivity no"},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":"Range: PeptideQuantification
Multivalued: True
name: has_peptide_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_peptide_quantifications\ndomain_of:\n- MetaproteomicsAnalysisActivity\nrange: PeptideQuantification\n\nURI: nmdc:has_raw_value
"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_raw_value/#properties","title":"Properties","text":"name: has raw value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nstring_serialization: '{has numeric value} {has unit}'\nalias: has_raw_value\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: string\n\nExample \"m\"
URI: nmdc:has_unit
"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_unit/#properties","title":"Properties","text":"name: has unit\ndescription: Example \"m\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_unit\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: string\n\nMain hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000989
"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":"name: hc_produced\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nmultivalued: false\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\n\nMain Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000988
"},{"location":"hcr/#inheritance","title":"Inheritance","text":"name: hcr\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n as a natural environmental feature containing large amounts of hydrocarbons at high\n concentrations potentially suitable for commercial exploitation. This term should\n not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n environments with currently limited commercial interest such as seeps, outcrops,\n gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nmultivalued: false\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\n\nOriginal formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS
URI: MIXS:0000406
"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":"name: hcr_fw_salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nmultivalued: false\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nGeological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period(geology)). If \"other\" is specified, please propose entry in \"additional info\" field_
URI: MIXS:0000993
"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":"name: hcr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nmultivalued: false\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\n\nOriginal pressure of the hydrocarbon resource
URI: MIXS:0000395
"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":"name: hcr_pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nmultivalued: false\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\n\nOriginal temperature of the hydrocarbon resource
URI: MIXS:0000393
"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":"name: hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nmultivalued: false\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\n\nMethods of conditioning or heating a room or building
URI: MIXS:0000766
"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":"Range: HeatCoolTypeEnum
Multivalued: True
name: heat_cool_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nmultivalued: true\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\n\nThe location of heat delivery within the room
URI: MIXS:0000810
"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":"name: heat_deliv_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nmultivalued: false\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\n\nThe method by which the heat is delivered through the system
URI: MIXS:0000812
"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":"name: heat_sys_deliv_meth\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nmultivalued: false\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\n\nThe heating system identifier
URI: MIXS:0000833
"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":"name: heat_system_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nmultivalued: false\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nHeavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.
URI: MIXS:0000652
"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: heavy_metals\nannotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nmultivalued: true\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\n\nReference or method used in determining heavy metals
URI: MIXS:0000343
"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":"name: heavy_metals_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nmultivalued: false\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average carpet fiber height in the indoor environment
URI: MIXS:0000167
"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":"name: height_carper_fiber\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nmultivalued: false\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000561
"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: herbicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of herbicide,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nmultivalued: true\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:highest_similarity_score
"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":"name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteQuantification\nrange: float\n\nThe purpose of the NMDC Schema is to define metadata for the National Microbiome Data Collaborative (NMDC). The NMDC is a multi-organizational effort to enable integrated microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.
The NMDC schema is used during the translation process to specify how metadata elements are related.
"},{"location":"horizon_meth/","title":"Slot: horizon_meth","text":"Reference or method used in determining the horizon
URI: MIXS:0000321
"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":"name: horizon_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nmultivalued: false\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nAge of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees
URI: MIXS:0000255
"},{"location":"host_age/#inheritance","title":"Inheritance","text":"name: host_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nmultivalued: false\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal body habitat where the sample was obtained from
URI: MIXS:0000866
"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":"name: host_body_habitat\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nmultivalued: false\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\n\nSubstance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon
URI: MIXS:0000888
"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":"name: host_body_product\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: Portion of mucus [fma66938]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nmultivalued: false\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nName of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
URI: MIXS:0000867
"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":"name: host_body_site\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nmultivalued: false\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nCore body temperature of the host when sample was collected
URI: MIXS:0000274
"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":"name: host_body_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nmultivalued: false\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe color of host
URI: MIXS:0000260
"},{"location":"host_color/#inheritance","title":"Inheritance","text":"name: host_color\nannotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nmultivalued: false\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\n\nCommon name of the host.
URI: MIXS:0000248
"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":"name: host_common_name\nannotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nmultivalued: false\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
URI: MIXS:0000869
"},{"location":"host_diet/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_diet\nannotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nmultivalued: true\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of dry mass
URI: MIXS:0000257
"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":"name: host_dry_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nmultivalued: false\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nFamilial relationships to other hosts in the same study; can include multiple relationships
URI: MIXS:0000872
"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_family_relation\nannotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\ndescription: Familial relationships to other hosts in the same study; can include\n multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nmultivalued: true\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\n\nObserved genotype
URI: MIXS:0000365
"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":"name: host_genotype\nannotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nmultivalued: false\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\n\nLiterature reference giving growth conditions of the host
URI: MIXS:0000871
"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":"name: host_growth_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nmultivalued: false\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe height of subject
URI: MIXS:0000264
"},{"location":"host_height/#inheritance","title":"Inheritance","text":"name: host_height\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nmultivalued: false\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nContent of last meal and time since feeding; can include multiple values
URI: MIXS:0000870
"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_last_meal\nannotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nmultivalued: true\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe length of subject
URI: MIXS:0000256
"},{"location":"host_length/#inheritance","title":"Inheritance","text":"name: host_length\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nmultivalued: false\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDescription of life stage of host
URI: MIXS:0000251
"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":"name: host_life_stage\nannotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nmultivalued: false\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:host_name
"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":"name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\nPhenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
URI: MIXS:0000874
"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":"name: host_phenotype\nannotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nmultivalued: false\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nGender or physical sex of the host.
URI: MIXS:0000811
"},{"location":"host_sex/#inheritance","title":"Inheritance","text":"name: host_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nmultivalued: false\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\n\nMorphological shape of host
URI: MIXS:0000261
"},{"location":"host_shape/#inheritance","title":"Inheritance","text":"name: host_shape\nannotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nmultivalued: false\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\n\nA unique identifier by which each subject can be referred to, de-identified.
URI: MIXS:0000861
"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":"name: host_subject_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nmultivalued: false\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.
URI: MIXS:0001318
"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_subspecf_genlin\nannotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nmultivalued: true\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\n\nThe growth substrate of the host.
URI: MIXS:0000252
"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":"name: host_substrate\nannotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nmultivalued: false\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
URI: MIXS:0001298
"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_symbiont\nannotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nmultivalued: true\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\n\nNCBI taxon id of the host, e.g. 9606
URI: MIXS:0000250
"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":"name: host_taxid\nannotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nmultivalued: false\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nTotal mass of the host at collection, the unit depends on host
URI: MIXS:0000263
"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":"name: host_tot_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nmultivalued: false\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of wet mass
URI: MIXS:0000567
"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":"name: host_wet_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nmultivalued: false\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nAmount of water vapour in the air, at the time of sampling
URI: MIXS:0000100
"},{"location":"humidity/#inheritance","title":"Inheritance","text":"name: humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nmultivalued: false\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000568
"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: humidity_regm\nannotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying degree of\n humidity; information about treatment involving use of growth hormones; should include\n amount of humidity administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end time\n of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nmultivalued: true\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nA unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
URI: nmdc:id
"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes Study A study summarizes the overall goal of a research initiative and outlines the... yes NamedThing a databased entity or concept/class no Activity a provence-generating activity yes Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes CollectingBiosamplesFromSite yes DataObject An object that primarily consists of symbols that represent information yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetatranscriptomeAssembly yes MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeAnnotationActivity yes MetatranscriptomeActivity A metatranscriptome activity that e yes MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... yes MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis yes ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... yes ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... yes MetabolomicsAnalysisActivity yes MetaproteomicsAnalysisActivity yes NomAnalysisActivity yes MaterialEntity no ProcessedSample yes AnalyticalSample yes Site yes PlannedProcess no OntologyClass yes EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample yes FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Biosample\n- Study\n- NamedThing\n- Activity\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nIdentifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects referenced
Examples of entities that require identifiers:
Identifiers should be:
See McMurry et al, PMID:28662064 for more desiderata.
"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"Following McMurry et al we adopt the use of prefixed identifiers
The syntax is:
Prefix:LocalId\nExamples:
These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these
All prefixes should be registered with a standard identifier prefix system. These include:
Registry entry: https://registry.identifiers.org/registry/biosample
Example ID/CURIE: BIOSAMPLE:SAMEA2397676
Resolving via identifiers.org: https://identifiers.org/BIOSAMPLE:SAMEA2397676
Resolving via nt2.net: http://n2t.net/BIOSAMPLE:SAMEA2397676
"},{"location":"identifiers/#gold-identifiers","title":"GOLD identifiers","text":"https://registry.identifiers.org/registry/gold
Example ID: GOLD:Gp0119849
Resolving via identifiers.org: https://identifiers.org/GOLD:Gp0119849
"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on http://obofoundry.org
For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007
KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.
The NMDC schema is annotated with the set of IDs that are allowed to act as primary keys for instances of each class.
For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY
The underlying yaml looks like this:
orthology group:\n is_a: functional annotation term\n description: >-\n A set of genes or gene products in which all members are orthologous\n id_prefixes:\n - KEGG.ORTHOLOGY ## KO number\n - EGGNOG\n - PFAM\n - TIGRFAM\n - SUPFAM\n - PANTHER.FAMILY\n exact_mappings:\n - biolink:GeneFamily\nThe full URLs for each is in the jsonld context file
"},{"location":"identifiers/#ids-minted-for-use-within-nmdc","title":"IDs minted for use within NMDC","text":"The NMDC schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification, which is discussed below.
NMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids, but it will require an update before it generates ids following the pattern specified below.
The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC schema and metadata team.
No matter where they are minted, all NMDC id values must match this abstract pattern:
nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\nThe abstract pattern has six parts, delimited by hyphens (unless otherwise specified):
nmdc: All NMDC identifiers will begin with this static prefix.
<typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.
<shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].
<blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.
<.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.
<_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.
The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.
^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\nWe try to reuse IDs as far as possible. For example, for any sample already in GOLD, we use the GOLD sample identifier, e.g. GOLD:Gb.....
"},{"location":"identifiers/#ids-generated-during-workflows","title":"IDs generated during workflows","text":"This section is in progress. See https://github.com/microbiomedata/nmdc-metadata/issues/195
All instances of OmicsProcessing have IDs. The policy for ID depends on the provider.
Currently metagenomics omics objects look like this:
id: \"gold:Gp0108335\"\n name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n has_input:\n - \"gold:Gb0108335\"\n part_of:\n - \"gold:Gs0112340\"\n has_output:\n - \"jgi:551a20d30d878525404e90d5\"\n omics_type: Metagenome\n type: \"nmdc:OmicsProcessing\"\n add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n processing_institution: \"Joint Genome Institute\"\n principal_investigator_name: \"Virginia Rich\"\nnote that we use re-using the GOLD ID rather than minting a new one
the linked data object uses a jgi prefix and an md5 hash
id: \"jgi:551a20d30d878525404e90d5\"\n name: \"8871.1.114459.GCCAAT.fastq.gz\"\n description: \"Raw sequencer read data\"\n file_size_bytes: 17586370657\n type: \"nmdc:DataObject\"\nnote that currently jgi is not registered and thus the ID is not resolvable
Currently metaproteomics omics objects look like this:
id: \"emsl:404590\"\n name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n part_of:\n - \"gold:Gs0110132\"\n has_output:\n - \"emsl:output_404590\"\n omics_type: Proteomics\n type: \"nmdc:OmicsProcessing\"\n instrument_name: \"VOrbiETD03\"\n processing_institution: \"Environmental Molecular Sciences Lab\"\nthis is suboptimal; emsl is not yet registered, and it's not clear that the integer is unique within emsl, let alone the nmdc subset
the output data objects are formed from these:
id: \"emsl:output_404590\"\n name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n file_size_bytes: 503296678\n type: \"nmdc:DataObject\"\nthe data objects use hashes (md5) prefixed with nmdc:
name: \"404590_resultant.tsv\"\n description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n file_size_bytes: 10948480\n type: \"nmdc:DataObject\"\n id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\nnote nmdc is not yet registered
Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.
The main entity we care about in these is the [gene product] https://microbiomedata.github.io/nmdc-metadata/docs/GeneProduct) ID (usually a protein), this is what functional annotation hangs off.
This is typically a protein encoded by a CDS, e.g.
Ga0185794_41 GeneMark.hmm-2 v1.05 CDS 48 1037 56.13 + 0 ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\nCurrently we are prefixing the ID field in GFF with nmdc, e.g. nmdc:Ga0185794_41_48_1037 as the protein ID
When converting col9 we ensure that each ID is correctly prefixed. So for example, we use KEGG.OTHOLOGY:K12960 not KO:K12960 as the former is the official prefix according to KEGG and identifiers.org
We will also later need a policy for IDs for the sequences in col1 (ie genome or transcript), please return later for more details...
"},{"location":"identifiers/#mixs-term-identifiers","title":"MIxS term identifiers","text":"We are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level.
Please check this section later
For now we place these in the nmdc namespaces, e.g
nmdc:alt
Please check this section later
"},{"location":"identifiers/#identifiers-and-semantic-web-uris","title":"Identifiers and semantic web URIs","text":"We produce a JSON-LD context with the schema:
When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs
"},{"location":"igsn_biosample_identifiers/","title":"Slot: igsn_biosample_identifiers","text":"A list of identifiers for the biosample from the IGSN database.
URI: nmdc:igsn_biosample_identifiers
"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nmultivalued: true\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:igsn_identifiers
"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\nA list of identifiers that relate the biosample to records in the IMG database.
URI: nmdc:img_identifiers
"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmultivalued: true\nalias: img_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\nURI: nmdc:inchi
"},{"location":"inchi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi/#properties","title":"Properties","text":"name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\ndomain_of:\n- ChemicalEntity\nrange: string\n\nURI: nmdc:inchi_key
"},{"location":"inchi_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi_key/#properties","title":"Properties","text":"name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\ndomain_of:\n- ChemicalEntity\nrange: string\n\nA distinguishable space within a structure, the purpose for which discrete areas of a building is used
URI: MIXS:0000763
"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":"name: indoor_space\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nmultivalued: false\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\n\nType of indoor surface
URI: MIXS:0000764
"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":"name: indoor_surf\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nmultivalued: false\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\n\nPercentage of industrial effluents received by wastewater treatment plant
URI: MIXS:0000662
"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":"name: indust_eff_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nmultivalued: false\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
URI: MIXS:0000664
"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: inorg_particles\nannotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nmultivalued: true\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe nucleotide base count number of input reads for QC analysis.
URI: nmdc:input_base_count
"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":"name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nURI: nmdc:input_contig_num
"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":"name: input_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nTotal mass of sample used in activity.
URI: nmdc:input_mass
"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":"name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n_TODO _
URI: nmdc:input_read_bases
"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":"name: input_read_bases\ndescription: 'TODO '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nThe sequence count number of input reads for QC analysis.
URI: nmdc:input_read_count
"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":"name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nURI: nmdc:insdc_analysis_identifiers
"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_analysis_identifiers\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\nURI: nmdc:insdc_assembly_identifiers
"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\nidentifiers for corresponding project in INSDC Bioproject
URI: nmdc:insdc_bioproject_identifiers
"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_bioproject_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\nidentifiers for corresponding sample in INSDC
URI: nmdc:insdc_biosample_identifiers
"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\nURI: nmdc:insdc_experiment_identifiers
"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_experiment_identifiers\ndomain_of:\n- OmicsProcessing\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\nAny identifier covered by the International Nucleotide Sequence Database Collaboration
URI: nmdc:insdc_identifiers
"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None OmicsProcessing insdc_analysis_identifiers None insdc_assembly_identifiers None MetagenomeAssembly, MetatranscriptomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\nsecondary identifiers for corresponding sample in INSDC
URI: nmdc:insdc_secondary_sample_identifiers
"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:(E|D|S)RS[0-9]{6,}$
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\nidentifiers for corresponding project in INSDC SRA / ENA
URI: nmdc:insdc_sra_ena_study_identifiers
"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\nThe recorded value at sampling time (power density)
URI: MIXS:0000168
"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":"name: inside_lux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nmultivalued: false\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe name of the instrument that was used for processing the sample.
URI: nmdc:instrument_name
"},{"location":"instrument_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no InstrumentValue no"},{"location":"instrument_name/#properties","title":"Properties","text":"name: instrument_name\ndescription: The name of the instrument that was used for processing the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_name\ndomain_of:\n- OmicsProcessing\n- InstrumentValue\nrange: string\n\nThe physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000813
"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":"name: int_wall_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nmultivalued: false\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\n\nfield describing aspect of the investigation/study to which the sample belongs
URI: nmdc:investigation_field
"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":"name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:is_balanced
"},{"location":"is_balanced/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_balanced/#properties","title":"Properties","text":"name: is_balanced\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_balanced\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_diastereoselective
"},{"location":"is_diastereoselective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_diastereoselective/#properties","title":"Properties","text":"name: is_diastereoselective\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_diastereoselective\ndomain_of:\n- Reaction\nrange: boolean\n\nFalse if includes R-groups
URI: nmdc:is_fully_characterized
"},{"location":"is_fully_characterized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_fully_characterized/#properties","title":"Properties","text":"name: is_fully_characterized\ndescription: False if includes R-groups\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_fully_characterized\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_stereo
"},{"location":"is_stereo/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_stereo/#properties","title":"Properties","text":"name: is_stereo\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stereo\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_transport
"},{"location":"is_transport/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_transport/#properties","title":"Properties","text":"name: is_transport\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_transport\ndomain_of:\n- Reaction\nrange: boolean\n\nList isotope exposure or addition applied to your sample.
URI: nmdc:isotope_exposure
"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":"Range: String
Recommended: True
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n labeled compounds\nexamples:\n- value: 13C glucose\n- value: H218O\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{termLabel} {[termID]}; {timestamp}'\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nInjection water breakthrough date per well following a secondary and/or tertiary recovery
URI: MIXS:0001010
"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":"name: iw_bt_date_well\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nmultivalued: false\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nProportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)
URI: MIXS:0000455
"},{"location":"iwf/#inheritance","title":"Inheritance","text":"name: iwf\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nmultivalued: false\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nidentifiers for entities according to JGI Portal
URI: nmdc:jgi_portal_identifiers
"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.
URI: nmdc:jgi_portal_study_identifiers
"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.proposal:\\d+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD API\n and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nmultivalued: true\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^jgi.proposal:\\d+$\n\nA list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO.
URI: nmdc:keywords
"},{"location":"keywords/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: keywords\ndescription: A list of keywords that used to associate the entity. Keywords SHOULD\n come from controlled vocabularies, including MESH, ENVO.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- dcterms:subject\nrank: 1000\nmultivalued: true\nalias: keywords\nrange: string\n\nShould use ISO 639-1 code e.g. \"en\", \"fr\"
URI: nmdc:language
"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":"name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language code\n\nThe last time the floor was cleaned (swept, mopped, vacuumed)
URI: MIXS:0000814
"},{"location":"last_clean/#inheritance","title":"Inheritance","text":"name: last_clean\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nmultivalued: false\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
URI: MIXS:0000009
"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":"name: lat_lon\nannotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nmultivalued: false\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\n\nlatitude
URI: wgs84:lat
"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":"name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\ndomain: GeolocationValue\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\nlime buffer capacity, determined after 30 minute incubation
URI: nmdc:lbc_thirty
"},{"location":"lbc_thirty/#inheritance","title":"Inheritance","text":"name: lbc_thirty\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nis_a: attribute\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nlime buffer capacity, determined at equilibrium after 5 day incubation
URI: nmdc:lbceq
"},{"location":"lbceq/#inheritance","title":"Inheritance","text":"name: lbceq\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nis_a: attribute\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:left_participants
"},{"location":"left_participants/#inheritance","title":"Inheritance","text":"Range: ReactionParticipant
Multivalued: True
name: left_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_participants\nmultivalued: true\nalias: left_participants\ndomain_of:\n- Reaction\nrange: ReactionParticipant\n\nURI: nmdc:library_preparation_kit
"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":"name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\nThis property links a database object to the set of DNA extractions within it.
URI: nmdc:library_preparation_set
"},{"location":"library_preparation_set/#inheritance","title":"Inheritance","text":"Range: LibraryPreparation
Multivalued: True
name: library_preparation_set\ndescription: This property links a database object to the set of DNA extractions within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- library_construction_set\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: library_preparation_set\ndomain_of:\n- Database\nrange: LibraryPreparation\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:library_type
"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":"name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\nMeasurement of light intensity
URI: MIXS:0000706
"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":"name: light_intensity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nmultivalued: false\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment(s) involving exposure to light, including both light intensity and quality.
URI: MIXS:0000569
"},{"location":"light_regm/#inheritance","title":"Inheritance","text":"name: light_regm\nannotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nmultivalued: false\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nApplication of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
URI: MIXS:0000769
"},{"location":"light_type/#inheritance","title":"Inheritance","text":"Range: LightTypeEnum
Multivalued: True
name: light_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n includes the use of both artificial light sources such as lamps and light fixtures,\n as well as natural illumination by capturing daylight. Can also include absence\n of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nmultivalued: true\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\n\nLink to additional analysis results performed on the sample
URI: MIXS:0000340
"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":"name: link_addit_analys\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nmultivalued: false\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\n\nLink to digitized soil maps or other soil classification information
URI: MIXS:0000329
"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":"name: link_class_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nmultivalued: false\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nLink to climate resource
URI: MIXS:0000328
"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":"name: link_climate_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nmultivalued: false\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nHydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000990
"},{"location":"lithology/#inheritance","title":"Inheritance","text":"name: lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nmultivalued: false\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\n\nSoil classification based on local soil classification system
URI: MIXS:0000330
"},{"location":"local_class/#inheritance","title":"Inheritance","text":"name: local_class\nannotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nmultivalued: false\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in determining the local soil classification
URI: MIXS:0000331
"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":"name: local_class_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nmultivalued: false\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:location
"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":"name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\nlongitude
URI: wgs84:long
"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":"name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\ndomain: GeolocationValue\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\nURI: nmdc:low_depth_contig_num
"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":"name: low_depth_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nConcentration of magnesium in the sample
URI: MIXS:0000431
"},{"location":"magnesium/#inheritance","title":"Inheritance","text":"name: magnesium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nmultivalued: false\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of MAGs analysis activities.
URI: nmdc:mags_activity_set
"},{"location":"mags_activity_set/#inheritance","title":"Inheritance","text":"Range: MagsAnalysisActivity
Multivalued: True
name: mags_activity_set\ndescription: This property links a database object to the set of MAGs analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: mags_activity_set\ndomain_of:\n- Database\nrange: MagsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:mags_list
"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":"Range: MagBin
Multivalued: True
name: mags_list\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: mags_list\ndomain_of:\n- MagsAnalysisActivity\nrange: MagBin\n\nConcentration of manganese in the sample
URI: nmdc:manganese
"},{"location":"manganese/#inheritance","title":"Inheritance","text":"name: manganese\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nis_a: attribute\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nidentifiers for entities according to MASSIVE
URI: nmdc:massive_identifiers
"},{"location":"massive_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain massive_study_identifiers identifiers for corresponding study in MASSIVE None Study"},{"location":"massive_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: massive_identifiers\ndescription: identifiers for entities according to MASSIVE\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: massive_identifiers\nrange: string\n\nidentifiers for corresponding study in MASSIVE
URI: nmdc:massive_study_identifiers
"},{"location":"massive_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^MASSIVE:
name: massive_study_identifiers\ndescription: identifiers for corresponding study in MASSIVE\ntodos:\n- prefix not defined yet\nexamples:\n- value: MASSIVE:MSV000090886\n description: MASSIVE id for MASSIVE's metabolomics analysis of Gb0305843, resolvable\n with prefix http://identifiers.org/massive/\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=83574f41458a4b259621d5c32a4d82f9\nrank: 1000\nis_a: study_identifiers\nmixins:\n- massive_identifiers\nmultivalued: true\nalias: massive_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: '^MASSIVE:'\n\nURI: nmdc:material_input
"},{"location":"material_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity yes ReactionActivity no"},{"location":"material_input/#properties","title":"Properties","text":"name: material_input\ntitle: material input\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_input\ndomain_of:\n- DissolvingActivity\n- ReactionActivity\nrange: MaterialSample\n\nURI: nmdc:material_output
"},{"location":"material_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity yes MaterialSamplingActivity yes ReactionActivity no"},{"location":"material_output/#properties","title":"Properties","text":"name: material_output\ntitle: material output\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_output\ndomain_of:\n- DissolvingActivity\n- MaterialSamplingActivity\n- ReactionActivity\nrange: MaterialSample\n\nURI: nmdc:material_sample_set
"},{"location":"material_sample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_sample_set/#properties","title":"Properties","text":"Range: MaterialSample
Multivalued: True
name: material_sample_set\ntitle: material sample set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: material_sample_set\ndomain_of:\n- Database\nrange: MaterialSample\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:material_sampling_activity_set
"},{"location":"material_sampling_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_sampling_activity_set/#properties","title":"Properties","text":"Range: MaterialSamplingActivity
Multivalued: True
name: material_sampling_activity_set\ntitle: material sampling activity set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: material_sampling_activity_set\ndomain_of:\n- Database\nrange: MaterialSamplingActivity\ninlined: true\ninlined_as_list: true\n\nThe maximum amount of people allowed in the indoor environment
URI: MIXS:0000229
"},{"location":"max_occup/#inheritance","title":"Inheritance","text":"name: max_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nmultivalued: false\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMD5 checksum of file (pre-compressed)
URI: nmdc:md5_checksum
"},{"location":"md5_checksum/#inheritance","title":"Inheritance","text":"name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\nMeasurement of mean friction velocity
URI: MIXS:0000498
"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nmultivalued: false\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of mean peak friction velocity
URI: MIXS:0000502
"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_peak_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nmultivalued: false\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nmechanical structure: a moving structure
URI: MIXS:0000815
"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":"name: mech_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nmultivalued: false\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\n\nInformation about any mechanical damage exerted on the plant; can include multiple damages and sites
URI: MIXS:0001052
"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mechanical_damage\nannotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nmultivalued: true\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:members_id
"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":"name: members_id\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\n\nthe specific metabolite identifier
URI: nmdc:metabolite_quantified
"},{"location":"metabolite_quantified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_quantified/#properties","title":"Properties","text":"name: metabolite_quantified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_quantified\ndomain_of:\n- MetaboliteQuantification\nrange: ChemicalEntity\n\nThis property links a database object to the set of metabolomics analysis activities.
URI: nmdc:metabolomics_analysis_activity_set
"},{"location":"metabolomics_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: MetabolomicsAnalysisActivity
Multivalued: True
name: metabolomics_analysis_activity_set\ndescription: This property links a database object to the set of metabolomics analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metabolomics_analysis_activity_set\ndomain_of:\n- Database\nrange: MetabolomicsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metagenome annotation activities.
URI: nmdc:metagenome_annotation_activity_set
"},{"location":"metagenome_annotation_activity_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeAnnotationActivity
Multivalued: True
name: metagenome_annotation_activity_set\ndescription: This property links a database object to the set of metagenome annotation\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_annotation_activity_set\ndomain_of:\n- Database\nrange: MetagenomeAnnotationActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:metagenome_annotation_id
"},{"location":"metagenome_annotation_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":"name: metagenome_annotation_id\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: WorkflowExecutionActivity\n\nURI: nmdc:metagenome_assembly_parameter
"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":"name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\nThis property links a database object to the set of metagenome assembly activities.
URI: nmdc:metagenome_assembly_set
"},{"location":"metagenome_assembly_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeAssembly
Multivalued: True
name: metagenome_assembly_set\ndescription: This property links a database object to the set of metagenome assembly\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_assembly_set\ndomain_of:\n- Database\nrange: MetagenomeAssembly\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metagenome sequencing activities.
URI: nmdc:metagenome_sequencing_activity_set
"},{"location":"metagenome_sequencing_activity_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeSequencingActivity
Multivalued: True
name: metagenome_sequencing_activity_set\ndescription: This property links a database object to the set of metagenome sequencing\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_sequencing_activity_set\ndomain_of:\n- Database\nrange: MetagenomeSequencingActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metaproteomics analysis activities.
URI: nmdc:metaproteomics_analysis_activity_set
"},{"location":"metaproteomics_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: MetaproteomicsAnalysisActivity
Multivalued: True
name: metaproteomics_analysis_activity_set\ndescription: This property links a database object to the set of metaproteomics analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metaproteomics_analysis_activity_set\ndomain_of:\n- Database\nrange: MetaproteomicsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metatranscriptome analysis activities.
URI: nmdc:metatranscriptome_activity_set
"},{"location":"metatranscriptome_activity_set/#inheritance","title":"Inheritance","text":"Range: MetatranscriptomeActivity
Multivalued: True
name: metatranscriptome_activity_set\ndescription: This property links a database object to the set of metatranscriptome\n analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metatranscriptome_activity_set\ndomain_of:\n- Database\nrange: MetatranscriptomeActivity\ninlined: true\ninlined_as_list: true\n\nMethane (gas) amount or concentration at the time of sampling
URI: MIXS:0000101
"},{"location":"methane/#inheritance","title":"Inheritance","text":"name: methane\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nmultivalued: false\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:mgnify_analysis_identifiers
"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nmultivalued: true\nalias: mgnify_analysis_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:mgnify_identifiers
"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\nidentifiers for corresponding project in MGnify
URI: nmdc:mgnify_project_identifiers
"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^mgnify.proj:[A-Z]+[0-9]+$
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nmultivalued: true\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\nReference or method used in determining microbial biomass carbon
URI: nmdc:micro_biomass_c_meth
"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nReference or method used in determining microbial biomass
URI: MIXS:0000339
"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":"name: micro_biomass_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nmultivalued: false\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining microbial biomass nitrogen
URI: nmdc:micro_biomass_n_meth
"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":"name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units
URI: MIXS:0000650
"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":"name: microbial_biomass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer. If you keep this, you would need to have correction\n factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nmultivalued: false\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_c
"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":"name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_n
"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":"name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nsmallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool
URI: nmdc:min_q_value
"},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":"name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n MSGFPlus tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\nInformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens
URI: MIXS:0000570
"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mineral_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple mineral\n nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nmultivalued: true\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAny other measurement performed or parameter collected, that is not listed here
URI: MIXS:0000752
"},{"location":"misc_param/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: misc_param\nannotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nmultivalued: true\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe last date on which the database information was modified.
URI: nmdc:mod_date
"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"mod_date/#properties","title":"Properties","text":"name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: string\n\nConcentration of n-alkanes; can include multiple n-alkanes
URI: MIXS:0000503
"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: n_alkanes\nannotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nmultivalued: true\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\n\nA human readable label for an entity
URI: nmdc:name
"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Protocol no QualityControlReport no NamedThing a databased entity or concept/class no PersonValue An attribute value representing a person yes Activity a provence-generating activity no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CollectingBiosamplesFromSite no DataObject An object that primarily consists of symbols that represent information yes Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no MaterialEntity no ProcessedSample no AnalyticalSample no Site no PlannedProcess no OntologyClass no EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"name/#properties","title":"Properties","text":"name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- Protocol\n- QualityControlReport\n- NamedThing\n- PersonValue\n- Activity\nrange: string\n\nURI: nmdc:ncbi_project_name
"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":"name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- OmicsProcessing\nrange: string\n\nURI: nmdc:ncbi_taxonomy_name
"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":"name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:neon_biosample_identifiers
"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nmultivalued: true\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:neon_deims_sdr_link
"},{"location":"neon_deims_sdr_link/#properties","title":"Properties","text":"name: neon_deims_sdr_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_deims_sdr_link\nrange: string\n\nURI: nmdc:neon_eco_type
"},{"location":"neon_eco_type/#properties","title":"Properties","text":"name: neon_eco_type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_eco_type\nrange: string\n\nidentifiers for entities according to NEON
URI: nmdc:neon_identifiers
"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\nURI: nmdc:neon_soil_type
"},{"location":"neon_soil_type/#properties","title":"Properties","text":"name: neon_soil_type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_soil_type\nrange: string\n\nURI: nmdc:neon_study_identifiers
"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nmultivalued: true\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nConcentration of nitrate in the sample
URI: MIXS:0000425
"},{"location":"nitrate/#inheritance","title":"Inheritance","text":"name: nitrate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nmultivalued: false\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrate nitrogen in the sample
URI: nmdc:nitrate_nitrogen
"},{"location":"nitrate_nitrogen/#inheritance","title":"Inheritance","text":"name: nitrate_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nis_a: attribute\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite in the sample
URI: MIXS:0000426
"},{"location":"nitrite/#inheritance","title":"Inheritance","text":"name: nitrite\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nmultivalued: false\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite nitrogen in the sample
URI: nmdc:nitrite_nitrogen
"},{"location":"nitrite_nitrogen/#inheritance","title":"Inheritance","text":"name: nitrite_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nis_a: attribute\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrogen (total)
URI: MIXS:0000504
"},{"location":"nitro/#inheritance","title":"Inheritance","text":"name: nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nmultivalued: false\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of natural organic matter (NOM) analysis activities.
URI: nmdc:nom_analysis_activity_set
"},{"location":"nom_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: NomAnalysisActivity
Multivalued: True
name: nom_analysis_activity_set\ndescription: This property links a database object to the set of natural organic matter\n (NOM) analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: nom_analysis_activity_set\ndomain_of:\n- Database\nrange: NomAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nAmount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;
URI: nmdc:non_microb_biomass
"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":"name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nReference or method used in determining biomass
URI: nmdc:non_microb_biomass_method
"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":"name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nInformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens
URI: MIXS:0000571
"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: non_min_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nmultivalued: true\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\n\nfrom study class
URI: nmdc:notes
"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":"name: notes\ndescription: from study class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
URI: MIXS:0000038
"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":"name: nucl_acid_amp\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nmultivalued: false\nalias: nucl_acid_amp\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
URI: MIXS:0000037
"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":"name: nucl_acid_ext\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the material separation to recover the nucleic acid\n fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nmultivalued: false\nalias: nucl_acid_ext\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:nucleic_acid_concentration
"},{"location":"nucleic_acid_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"nucleic_acid_concentration/#properties","title":"Properties","text":"name: nucleic_acid_concentration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: nucleic_acid_concentration\ndomain_of:\n- ProcessedSample\nrange: InstrumentValue\n\nURI: nmdc:nucleic_acid_sequence_source_field
"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":"name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:num_16s
"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":"name: num_16s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:num_23s
"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":"name: num_23s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:num_5s
"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":"name: num_5s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\n\nThe sequence count number of input reads aligned to assembled contigs.
URI: nmdc:num_aligned_reads
"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":"name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sequence count number of input reads for assembly.
URI: nmdc:num_input_reads
"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":"name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nURI: nmdc:num_t_rna
"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":"name: num_t_rna\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:number_of_contig
"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":"name: number_of_contig\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\n\nThe number of pets residing in the sampled space
URI: MIXS:0000231
"},{"location":"number_pets/#inheritance","title":"Inheritance","text":"name: number_pets\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nmultivalued: false\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of plant(s) in the sampling space
URI: MIXS:0000230
"},{"location":"number_plants/#inheritance","title":"Inheritance","text":"name: number_plants\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nmultivalued: false\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of individuals currently occupying in the sampling location
URI: MIXS:0000232
"},{"location":"number_resident/#inheritance","title":"Inheritance","text":"name: number_resident\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nmultivalued: false\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nApplies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types
URI: nmdc:object_set
"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database activity_set This property links a database object to the set of workflow activities WorkflowExecutionActivity Database mags_activity_set This property links a database object to the set of MAGs analysis activities MagsAnalysisActivity Database metabolomics_analysis_activity_set This property links a database object to the set of metabolomics analysis act... MetabolomicsAnalysisActivity Database metaproteomics_analysis_activity_set This property links a database object to the set of metaproteomics analysis a... MetaproteomicsAnalysisActivity Database metagenome_annotation_activity_set This property links a database object to the set of metagenome annotation act... MetagenomeAnnotationActivity Database metagenome_assembly_set This property links a database object to the set of metagenome assembly activ... MetagenomeAssembly Database metagenome_sequencing_activity_set This property links a database object to the set of metagenome sequencing act... MetagenomeSequencingActivity Database metatranscriptome_activity_set This property links a database object to the set of metatranscriptome analysi... MetatranscriptomeActivity Database read_qc_analysis_activity_set This property links a database object to the set of read QC analysis activiti... ReadQcAnalysisActivity Database read_based_taxonomy_analysis_activity_set This property links a database object to the set of read based analysis activ... ReadBasedTaxonomyAnalysisActivity Database nom_analysis_activity_set This property links a database object to the set of natural organic matter (N... NomAnalysisActivity Database omics_processing_set This property links a database object to the set of omics processings within ... OmicsProcessing Database pooling_set Pooling Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database extraction_set This property links a database object to the set of extractions within it Extraction Database library_preparation_set This property links a database object to the set of DNA extractions within it LibraryPreparation Database"},{"location":"object_set/#properties","title":"Properties","text":"Range: String
Multivalued: True
Mixin: True
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n This is necessary in a json document to provide context for a list, and to allow\n for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\ndomain: Database\nmultivalued: true\nalias: object_set\nrange: string\ninlined_as_list: true\n\nThe scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.
URI: nmdc:objective
"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":"name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nmultivalued: false\nalias: objective\ndomain_of:\n- Study\nrange: string\n\nAverage number of occupants at time of sampling per square footage
URI: MIXS:0000217
"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":"name: occup_density_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nmultivalued: false\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of documentation of occupancy
URI: MIXS:0000816
"},{"location":"occup_document/#inheritance","title":"Inheritance","text":"name: occup_document\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nmultivalued: false\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\n\nNumber of occupants present at time of sample within the given space
URI: MIXS:0000772
"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":"name: occup_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nmultivalued: false\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:omics_processing_identifiers
"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: omics_processing_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of omics processings within it.
URI: nmdc:omics_processing_set
"},{"location":"omics_processing_set/#inheritance","title":"Inheritance","text":"Range: OmicsProcessing
Multivalued: True
name: omics_processing_set\ndescription: This property links a database object to the set of omics processings\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: omics_processing_set\ndomain_of:\n- Database\nrange: OmicsProcessing\ninlined: true\ninlined_as_list: true\n\nThe type of omics data
URI: nmdc:omics_type
"},{"location":"omics_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"omics_type/#properties","title":"Properties","text":"name: omics_type\ndescription: The type of omics data\nnotes:\n- was the range string at one point? the values in MongoDB don't look like NMDC classes\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: omics_type\ndomain_of:\n- OmicsProcessing\nrange: ControlledTermValue\n\nThe ORCID of a person.
URI: nmdc:orcid
"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":"name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: PersonValue\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\nConcentration of organic carbon
URI: MIXS:0000508
"},{"location":"org_carb/#inheritance","title":"Inheritance","text":"name: org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nmultivalued: false\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nIf qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)
URI: MIXS:0000099
"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":"name: org_count_qpcr_info\nannotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nmultivalued: false\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of organic matter
URI: MIXS:0000204
"},{"location":"org_matter/#inheritance","title":"Inheritance","text":"name: org_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nmultivalued: false\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of organic nitrogen
URI: MIXS:0000205
"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":"name: org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nmultivalued: false\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod used for obtaining organic nitrogen
URI: nmdc:org_nitro_method
"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":"name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nConcentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.
URI: MIXS:0000665
"},{"location":"org_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: org_particles\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nmultivalued: true\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
URI: MIXS:0000103
"},{"location":"organism_count/#inheritance","title":"Inheritance","text":"Range: QuantityValue
Multivalued: True
name: organism_count\nannotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n or area of sample, should include name of organism followed by count. The method\n that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nmultivalued: true\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOther treatments applied to your samples that are not applicable to the provided fields
URI: nmdc:other_treatment
"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":"Range: String
Recommended: True
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n provided fields\ntitle: other treatments\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nAfter QC analysis nucleotide base count number.
URI: nmdc:output_base_count
"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":"name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nTODO
URI: nmdc:output_read_bases
"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":"name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nAfter QC analysis sequence count number.
URI: nmdc:output_read_count
"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":"name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nDepth of the original oil water contact (OWC) zone (average) (m TVDSS)
URI: MIXS:0000405
"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":"name: owc_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nmultivalued: false\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOxygenation status of sample
URI: MIXS:0000753
"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":"name: oxy_stat_samp\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nmultivalued: false\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\n\nOxygen (gas) amount or concentration at the time of sampling
URI: MIXS:0000104
"},{"location":"oxygen/#inheritance","title":"Inheritance","text":"name: oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nmultivalued: false\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nLinks a resource to another resource that either logically or physically includes it.
URI: dcterms:isPartOf
"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment yes Study A study summarizes the overall goal of a research initiative and outlines the... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"part_of/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\ndomain: NamedThing\nslot_uri: dcterms:isPartOf\nmultivalued: true\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Biosample\n- Study\n- OmicsProcessing\n- WorkflowExecutionActivity\nrange: NamedThing\n\nConcentration of particulate organic carbon
URI: MIXS:0000515
"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":"name: part_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nmultivalued: false\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of particulate organic nitrogen
URI: MIXS:0000719
"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":"name: part_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nmultivalued: false\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nParticles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values
URI: MIXS:0000206
"},{"location":"particle_class/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: particle_class\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nmultivalued: true\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\n\nDescription of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
URI: MIXS:0000049
"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":"name: pcr_cond\nannotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nmultivalued: false\nalias: pcr_cond\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:pcr_cycles
"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":"name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\nPCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
URI: MIXS:0000046
"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":"name: pcr_primers\nannotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n locus or subfragment. This field should contain all the primers used for a single\n PCR reaction if multiple forward or reverse primers are present in a single PCR\n reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nmultivalued: false\nalias: pcr_primers\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:peptide_sequence
"},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":"name: peptide_sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\ncount of peptide sequences grouped to the best_protein
URI: nmdc:peptide_sequence_count
"},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":"name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nsum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file
URI: nmdc:peptide_spectral_count
"},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":"name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:peptide_sum_masic_abundance
"},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":"name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\nMeasure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability(earth_sciences))_
URI: MIXS:0000404
"},{"location":"permeability/#inheritance","title":"Inheritance","text":"name: permeability\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nmultivalued: false\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
URI: MIXS:0000754
"},{"location":"perturbation/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: perturbation\nannotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time of the\n entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nmultivalued: true\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens
URI: MIXS:0000573
"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pesticide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of insecticides; should include\n the name of pesticide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nmultivalued: true\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of petroleum hydrocarbon
URI: MIXS:0000516
"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":"name: petroleum_hydrocarb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nmultivalued: false\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nPh measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
URI: MIXS:0001001
"},{"location":"ph/#inheritance","title":"Inheritance","text":"name: ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nmultivalued: false\nalias: ph\ndomain_of:\n- Biosample\nrange: double\n\nReference or method used in determining ph
URI: MIXS:0001106
"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":"name: ph_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nmultivalued: false\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen
URI: MIXS:0001056
"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: ph_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n of ph of the growth media, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nmultivalued: true\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of phaeopigments; can include multiple phaeopigments
URI: MIXS:0000180
"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phaeopigments\nannotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nmultivalued: true\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.
URI: nmdc:phase
"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
Maximum Value: 2
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\nConcentration of phosphate
URI: MIXS:0000505
"},{"location":"phosphate/#inheritance","title":"Inheritance","text":"name: phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nmultivalued: false\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of phospholipid fatty acids; can include multiple values
URI: MIXS:0000181
"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phosplipid_fatt_acid\nannotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nmultivalued: true\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of photon flux
URI: MIXS:0000725
"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":"name: photon_flux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nmultivalued: false\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSpecification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
URI: MIXS:0001057
"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":"name: plant_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n liquid culture medium. Recommended value is a specific value from EO:plant growth\n medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nmultivalued: false\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nSubstance produced by the plant, where the sample was obtained from
URI: MIXS:0001058
"},{"location":"plant_product/#inheritance","title":"Inheritance","text":"name: plant_product\nannotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nmultivalued: false\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\n\nSex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.
URI: MIXS:0001059
"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":"name: plant_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nmultivalued: false\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\n\nName of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.
URI: MIXS:0001060
"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":"name: plant_struc\nannotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nmultivalued: false\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nPollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
URI: MIXS:0000107
"},{"location":"pollutants/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pollutants\nannotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n sampling; can report multiple pollutants by entering numeric values preceded by\n name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nmultivalued: true\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\n\nIndicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
URI: MIXS:0000325
"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":"name: pool_dna_extracts\nannotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nmultivalued: false\nalias: pool_dna_extracts\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:pooling_set
"},{"location":"pooling_set/#inheritance","title":"Inheritance","text":"Range: Pooling
Multivalued: True
name: pooling_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: pooling_set\ndomain_of:\n- Database\nrange: Pooling\ninlined: true\ninlined_as_list: true\n\nPorosity of deposited sediment is volume of voids divided by the total volume of sample
URI: MIXS:0000211
"},{"location":"porosity/#inheritance","title":"Inheritance","text":"name: porosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nmultivalued: false\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of potassium in the sample
URI: MIXS:0000430
"},{"location":"potassium/#inheritance","title":"Inheritance","text":"name: potassium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nmultivalued: false\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTemperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)
URI: MIXS:0000127
"},{"location":"pour_point/#inheritance","title":"Inheritance","text":"name: pour_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nmultivalued: false\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe process of pre-treatment removes materials that can be easily collected from the raw wastewater
URI: MIXS:0000348
"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":"name: pre_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nmultivalued: false\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nAll metadata gathered and stored by the NMDC community must validate against the nmdc-schema.
"},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-expressed-in-the-linkml-schema-language","title":"The nmdc-schema is expressed in the LinkML schema language.","text":"LinkML uses structures like classes, slots (for relationships and properties), types and enumerations. People with object-oriented programming experience might find this familiar.
"},{"location":"prefixes_curies_ids_mappings_etc/#the-name-linkml-indicates-that-its-a-modeling-language-for-linked-data","title":"The name \"LinkML\" indicates that it's' a modeling language for linked data.","text":"LinkML schemas generally make good use of terminology from external resources, especially ontologies, especially those from the OBO Foundry. In return, LinkML schema elements and the corresponding data should be interoperable with other ontologies and semantic databases.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-element-identifiers-in-the-schema-with-uris-and-curies","title":"Asserting element identifiers in the schema with URIs and CURIEs","text":"One consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.
Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the nmdc-schema","text":"As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.
Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.
Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.
When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.
A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs.
pooling_set:\n - id: pooling:1\n inputs:\n - biosample:1\n - biosample:2\n - biosample:3\n - id: pooling:2\n inputs:\n - biosample:4\n - biosample:5\n - biosample:6\nHere we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.
In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.
Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.
biosample_set:\n - id: biosample:1\n gold_biosample_identifiers:\n - gold:1\n - gold:2\nIn this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.
"},{"location":"prefixes_curies_ids_mappings_etc/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )
All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.
Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.
Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.
If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'
make gen-project)default_curi_maps any more--emsl-biosample-uuid-replacement in anyuri-strings-to-iris--salvage-prefix added by migration-recursionpatterns and id_prefixeswarning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)
warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)
"},{"location":"prefixes_curies_ids_mappings_etc/#unresolved","title":"unresolved","text":"make better use of id prefixes?
todo what reference ontologies do we want to include in a graph database?
could federate uniprot
gen-prefix-map
emits JSON content into a file with teh .yaml extension by default
doesn't look like all the emit_prefixes are making it into the OWL output
two graphdb endpoints: http://3.236.215.220:7200/sparql (switch to port 80) and https://graphdb-dev.microbiomedata.org/
make squeaky-clean does not include mixs-yaml-clean, so that mixs.yaml isn't unnecessarily regeneratedThe type and number of animals or insects present in the sampling space.
URI: MIXS:0000819
"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^(cat|dog|rodent|snake|other);\\d+$
name: pres_animal_insect\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nmultivalued: false\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\nPressure to which the sample is subject to, in atmospheres
URI: MIXS:0000412
"},{"location":"pressure/#inheritance","title":"Inheritance","text":"name: pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nmultivalued: false\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining previous land use and dates
URI: MIXS:0000316
"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":"name: prev_land_use_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nmultivalued: false\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\n\nPrevious land use and dates
URI: MIXS:0000315
"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":"name: previous_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nmultivalued: false\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of primary production, generally measured as isotope uptake
URI: MIXS:0000728
"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":"name: primary_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nmultivalued: false\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed
URI: MIXS:0000349
"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":"name: primary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nmultivalued: false\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nPrincipal Investigator who led the study and/or generated the dataset.
URI: nmdc:principal_investigator
"},{"location":"principal_investigator/#inheritance","title":"Inheritance","text":"name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nis_a: attribute\nalias: principal_investigator\ndomain_of:\n- Study\n- OmicsProcessing\nrange: PersonValue\n\nThis property links a database object to the set of processed samples within it.
URI: nmdc:processed_sample_set
"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":"Range: ProcessedSample
Multivalued: True
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\ninlined: true\ninlined_as_list: true\n\nThe organization that processed the sample.
URI: nmdc:processing_institution
"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"processing_institution/#properties","title":"Properties","text":"name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- Extraction\n- LibraryPreparation\n- OmicsProcessing\nrange: processing_institution_enum\n\nOil and/or gas production rates per well (e.g. 524 m3 / day)
URI: MIXS:0000452
"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":"name: prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nmultivalued: false\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDate of field's first production
URI: MIXS:0001008
"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":"name: prod_start_date\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nmultivalued: false\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nA url that points to an image of a person.
URI: nmdc:profile_image_url
"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":"name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: PersonValue\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\nCross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
URI: MIXS:0001084
"},{"location":"profile_position/#inheritance","title":"Inheritance","text":"name: profile_position\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nmultivalued: false\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\n\nProposal IDs or names associated with dataset
URI: nmdc:project_id
"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nURI: nmdc:proport_woa_temperature
"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":"name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:proposal_dna
"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:proposal_rna
"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nsum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file
URI: nmdc:protein_spectral_count
"},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":"name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:protein_sum_masic_abundance
"},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":"name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the best protein from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nURI: nmdc:protocol_link
"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no PlannedProcess no Pooling physical combination of several instances of like material no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"protocol_link/#properties","title":"Properties","text":"name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- Extraction\n- PlannedProcess\nrange: Protocol\n\nOne or more DOIs that links a study, or similar entity, to a publication.
URI: nmdc:publication_dois
"},{"location":"publication_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: publication_dois\ndescription: One or more DOIs that links a study, or similar entity, to a publication.\nexamples:\n- value: doi:10.1126/science.1058040\n description: publication_dois link to a prose document, preferably a peer-reviewed\n journal article. Should not be used to link to datasets or administrative information\n like funding requests or awards\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: publication_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nA list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.
URI: nmdc:publications
"},{"location":"publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"publications/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: publications\ndescription: A list of publications that are associated with the entity. The publications\n SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: publications\ndomain_of:\n- Study\nrange: string\n\nThe quadrant position of the sampling room within the building
URI: MIXS:0000820
"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":"name: quad_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nmultivalued: false\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\n\nURI: nmdc:quality_control_report
"},{"location":"quality_control_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"quality_control_report/#properties","title":"Properties","text":"name: quality_control_report\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: quality_control_report\ndomain_of:\n- Extraction\nrange: QualityControlReport\n\nInformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens
URI: MIXS:0000575
"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: radiation_regm\nannotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n to a particular radiation regimen; should include the radiation type, amount or\n intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nmultivalued: true\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000576
"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: rainfall_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to a given amount of\n rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nmultivalued: true\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:reaction_activity_set
"},{"location":"reaction_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"reaction_activity_set/#properties","title":"Properties","text":"Range: ReactionActivity
Multivalued: True
name: reaction_activity_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: reaction_activity_set\ndomain_of:\n- Database\nrange: ReactionActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:reaction_aided_by
"},{"location":"reaction_aided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity no"},{"location":"reaction_aided_by/#properties","title":"Properties","text":"name: reaction_aided_by\ntitle: reaction aided by\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker\nrank: 1000\nalias: reaction_aided_by\ndomain_of:\n- ReactionActivity\nrange: LabDevice\ninlined: true\n\nURI: nmdc:reaction_temperature
"},{"location":"reaction_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity no"},{"location":"reaction_temperature/#properties","title":"Properties","text":"name: reaction_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: reaction_temperature\ndomain_of:\n- ReactionActivity\nrange: string\n\nURI: nmdc:reaction_time
"},{"location":"reaction_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity yes"},{"location":"reaction_time/#properties","title":"Properties","text":"name: reaction_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: reaction_time\ndomain_of:\n- ReactionActivity\nrange: QuantityValue\ninlined: true\n\nAnaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage
URI: MIXS:0000350
"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":"name: reactor_type\nannotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nmultivalued: false\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of read based analysis activities.
URI: nmdc:read_based_taxonomy_analysis_activity_set
"},{"location":"read_based_taxonomy_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: ReadBasedTaxonomyAnalysisActivity
Multivalued: True
name: read_based_taxonomy_analysis_activity_set\ndescription: This property links a database object to the set of read based analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: read_based_taxonomy_analysis_activity_set\ndomain_of:\n- Database\nrange: ReadBasedTaxonomyAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of read QC analysis activities.
URI: nmdc:read_qc_analysis_activity_set
"},{"location":"read_qc_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: ReadQcAnalysisActivity
Multivalued: True
name: read_qc_analysis_activity_set\ndescription: This property links a database object to the set of read QC analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: read_qc_analysis_activity_set\ndomain_of:\n- Database\nrange: ReadQcAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:read_qc_analysis_statistic
"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":"name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\nRedox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
URI: MIXS:0000182
"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":"name: redox_potential\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nmultivalued: false\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nPartial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
URI: MIXS:0000121
"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":"name: rel_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nmultivalued: false\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe recorded outside relative humidity value at the time of sampling
URI: MIXS:0000188
"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":"name: rel_humidity_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nmultivalued: false\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe sampling location within the train car
URI: MIXS:0000821
"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":"name: rel_samp_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nmultivalued: false\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\n\nIdentifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.
URI: nmdc:related_identifiers
"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":"name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\nURI: nmdc:relevant_protocols
"},{"location":"relevant_protocols/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"relevant_protocols/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: relevant_protocols\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: relevant_protocols\ndomain_of:\n- Study\nrange: string\n\nIf sending biological replicates, indicate the rep number here.
URI: nmdc:replicate_number
"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":"Range: String
Recommended: True
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nName of the reservoir (e.g. Carapebus)
URI: MIXS:0000303
"},{"location":"reservoir/#inheritance","title":"Inheritance","text":"name: reservoir\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nmultivalued: false\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000134
"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":"name: resins_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nmultivalued: false\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:right_participants
"},{"location":"right_participants/#inheritance","title":"Inheritance","text":"Range: ReactionParticipant
Multivalued: True
name: right_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_participants\nmultivalued: true\nalias: right_participants\ndomain_of:\n- Reaction\nrange: ReactionParticipant\n\n260/280 measurement of RNA sample purity
URI: nmdc:rna_absorb1
"},{"location":"rna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n260/230 measurement of RNA sample purity
URI: nmdc:rna_absorb2
"},{"location":"rna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\nProvide information on the site your RNA sample was collected from
URI: nmdc:rna_collect_site
"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_concentration
"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nTube or plate (96-well)
URI: nmdc:rna_cont_type
"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:rna_cont_well
"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:rna_container_id
"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:rna_isolate_meth
"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:rna_organisms
"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_project_contact
"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_samp_id
"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nSolution in which the RNA sample has been suspended
URI: nmdc:rna_sample_format
"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":"Range: RnaSampleFormatEnum
Recommended: True
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: rna_sample_format_enum\nrecommended: true\n\nGive the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:rna_sample_name
"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nURI: nmdc:rna_seq_project
"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_name
"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_pi
"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_volume
"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nThe rate at which outside air replaces indoor air in a given space
URI: MIXS:0000169
"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":"name: room_air_exch_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nmultivalued: false\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure
URI: MIXS:0000233
"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":"name: room_architec_elem\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nmultivalued: false\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\n\nThe condition of the room at the time of sampling
URI: MIXS:0000822
"},{"location":"room_condt/#inheritance","title":"Inheritance","text":"name: room_condt\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nmultivalued: false\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\n\nList of rooms connected to the sampling room by a doorway
URI: MIXS:0000826
"},{"location":"room_connected/#inheritance","title":"Inheritance","text":"name: room_connected\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nmultivalued: false\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\n\nThe total count of rooms in the built structure including all room types
URI: MIXS:0000234
"},{"location":"room_count/#inheritance","title":"Inheritance","text":"name: room_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nmultivalued: false\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe length, width and height of sampling room
URI: MIXS:0000192
"},{"location":"room_dim/#inheritance","title":"Inheritance","text":"name: room_dim\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nmultivalued: false\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\n\nDistance between doors (meters) in the hallway between the sampling room and adjacent rooms
URI: MIXS:0000193
"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":"name: room_door_dist\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nmultivalued: false\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) sharing a door with the sampling room
URI: MIXS:0000242
"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":"name: room_door_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nmultivalued: false\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) located in the same hallway as sampling room
URI: MIXS:0000238
"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":"name: room_hallway\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nmultivalued: false\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe position of the room within the building
URI: MIXS:0000823
"},{"location":"room_loc/#inheritance","title":"Inheritance","text":"name: room_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nmultivalued: false\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\n\nThe history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
URI: MIXS:0000235
"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":"name: room_moist_dam_hist\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nmultivalued: false\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\n\nThe net floor area of sampling room. Net area excludes wall thicknesses
URI: MIXS:0000194
"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":"name: room_net_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nmultivalued: false\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\n\nCount of room occupancy at time of sampling
URI: MIXS:0000236
"},{"location":"room_occup/#inheritance","title":"Inheritance","text":"name: room_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nmultivalued: false\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe horizontal sampling position in the room relative to architectural elements
URI: MIXS:0000824
"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":"name: room_samp_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nmultivalued: false\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\n\nThe main purpose or activity of the sampling room. A room is any distinguishable space within a structure
URI: MIXS:0000825
"},{"location":"room_type/#inheritance","title":"Inheritance","text":"name: room_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nmultivalued: false\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\n\nVolume of sampling room
URI: MIXS:0000195
"},{"location":"room_vol/#inheritance","title":"Inheritance","text":"name: room_vol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nmultivalued: false\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) sharing a wall with the sampling room
URI: MIXS:0000243
"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":"name: room_wall_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nmultivalued: false\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\n\nNumber of windows in the room
URI: MIXS:0000237
"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":"name: room_window_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nmultivalued: false\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\n\nRelevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.
URI: MIXS:0001061
"},{"location":"root_cond/#inheritance","title":"Inheritance","text":"name: root_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nmultivalued: false\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nSource of organic carbon in the culture rooting medium; e.g. sucrose.
URI: MIXS:0000577
"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":"name: root_med_carbon\nannotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nmultivalued: false\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).
URI: MIXS:0000578
"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":"name: root_med_macronutr\nannotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nmultivalued: false\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).
URI: MIXS:0000579
"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":"name: root_med_micronutr\nannotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nmultivalued: false\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\n\npH measurement of the culture rooting medium; e.g. 5.5.
URI: MIXS:0001062
"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":"name: root_med_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nmultivalued: false\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nGrowth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.
URI: MIXS:0000581
"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":"name: root_med_regl\nannotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nmultivalued: false\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\n\nSpecification of the solidifying agent in the culture rooting medium; e.g. agar.
URI: MIXS:0001063
"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":"name: root_med_solid\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nmultivalued: false\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\n\nOrganic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).
URI: MIXS:0000580
"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":"name: root_med_suppl\nannotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nmultivalued: false\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.
URI: MIXS:0000183
"},{"location":"salinity/#inheritance","title":"Inheritance","text":"name: salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n While salinity can be measured by a complete chemical analysis, this method is difficult\n and time consuming. More often, it is instead derived from the conductivity measurement.\n This is known as practical salinity. These derivations compare the specific conductance\n of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nmultivalued: false\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCategorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline
URI: nmdc:salinity_category
"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":"name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining salinity
URI: MIXS:0000341
"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":"name: salinity_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nmultivalued: false\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens
URI: MIXS:0000582
"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: salt_regm\nannotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n and soil growth media; should include the name of salt, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nmultivalued: true\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nReason for the sample
URI: MIXS:0000860
"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":"name: samp_capt_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nmultivalued: false\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\n\nThe device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
URI: MIXS:0000002
"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":"name: samp_collec_device\nannotations:\n expected_value:\n tag: expected_value\n value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nmultivalued: false\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\n\nThe method employed for collecting the sample.
URI: MIXS:0001225
"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":"name: samp_collec_method\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nmultivalued: false\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\n\nSampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001015
"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":"name: samp_collect_point\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry in\n \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nmultivalued: false\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\n\nStage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.
URI: MIXS:0000249
"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":"name: samp_dis_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nmultivalued: false\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\n\nThe floor of the building, where the sampling room is located
URI: MIXS:0000828
"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":"name: samp_floor\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nmultivalued: false\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\n\nMetal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays
URI: MIXS:0000136
"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":"name: samp_loc_corr_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short term\n rates and for that reason they are preferred during reporting. In the case of suspected\n MIC, corrosion rate measurements at the time of sampling might provide insights\n into the involvement of certain microbial community members in MIC as well as potential\n microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nmultivalued: false\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\n\nA brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.
URI: MIXS:0000016
"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":"name: samp_mat_process\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A brief description of any processing applied to the sample during or\n after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nmultivalued: false\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nIn non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000413
"},{"location":"samp_md/#inheritance","title":"Inheritance","text":"name: samp_md\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n MD is the length of trajectory of the borehole measured from the same reference\n or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nmultivalued: false\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nA local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.
URI: MIXS:0001107
"},{"location":"samp_name/#inheritance","title":"Inheritance","text":"name: samp_name\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A local identifier or name that for the material sample used for extracting\n nucleic acids, and subsequent sequencing. It can refer either to the original material\n collected or to any derived sub-samples. It can have any format, but we suggest\n that you make it concise, unique and consistent within your lab, and as informative\n as possible. INSDC requires every sample name from a single Submitter to be unique.\n Use of a globally unique identifier for the field source_mat_id is recommended in\n addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nmultivalued: false\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\n\nPreservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
URI: MIXS:0000463
"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":"name: samp_preserv\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nmultivalued: false\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\n\nSampling room number. This ID should be consistent with the designations on the building floor plans
URI: MIXS:0000244
"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":"name: samp_room_id\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nmultivalued: false\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
URI: MIXS:0000001
"},{"location":"samp_size/#inheritance","title":"Inheritance","text":"name: samp_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nmultivalued: false\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.
URI: MIXS:0000216
"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: samp_sort_meth\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers in\n diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nmultivalued: true\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nDuration for which the sample was stored
URI: MIXS:0000116
"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":"name: samp_store_dur\nannotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nmultivalued: false\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\n\nLocation at which sample was stored, usually name of a specific freezer/room
URI: MIXS:0000755
"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":"name: samp_store_loc\nannotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nmultivalued: false\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\n\nTemperature at which sample was stored, e.g. -80 degree Celsius
URI: MIXS:0000110
"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":"name: samp_store_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nmultivalued: false\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nName of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000999
"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":"name: samp_subtype\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nmultivalued: false\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\n\nNCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.
URI: MIXS:0001320
"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":"name: samp_taxon_id\nannotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\ndescription: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample.\n Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nmultivalued: false\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nThe recent and long term history of outside sampling
URI: MIXS:0000196
"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":"name: samp_time_out\nannotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nmultivalued: false\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\n\nSample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)
URI: MIXS:0000410
"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":"name: samp_transport_cond\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nmultivalued: false\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nDepth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m
URI: MIXS:0000409
"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":"name: samp_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nmultivalued: false\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
URI: MIXS:0000998
"},{"location":"samp_type/#inheritance","title":"Inheritance","text":"name: samp_type\nannotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n package, samples include types like core, rock trimmings, drill cuttings, piping\n section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n injected water, swabs, etc. For the Food Package, samples are usually categorized\n as food, body products or tissues, or environmental material. This field accepts\n terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nmultivalued: false\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nVolume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
URI: MIXS:0000111
"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":"name: samp_vol_we_dna_ext\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n extraction. Note: total sample collected should be entered under the term Sample\n Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nmultivalued: false\nalias: samp_vol_we_dna_ext\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: QuantityValue\n\nThe weather on the sampling day
URI: MIXS:0000827
"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":"name: samp_weather\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nmultivalued: false\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\n\nName of the well (e.g. BXA1123) where sample was taken
URI: MIXS:0000296
"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":"name: samp_well_name\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nmultivalued: false\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:sample_collection_day
"},{"location":"sample_collection_day/#properties","title":"Properties","text":"name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\nURI: nmdc:sample_collection_hour
"},{"location":"sample_collection_hour/#properties","title":"Properties","text":"name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\nURI: nmdc:sample_collection_minute
"},{"location":"sample_collection_minute/#properties","title":"Properties","text":"name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\nURI: nmdc:sample_collection_month
"},{"location":"sample_collection_month/#properties","title":"Properties","text":"name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\nURI: nmdc:sample_collection_site
"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":"name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:sample_collection_year
"},{"location":"sample_collection_year/#properties","title":"Properties","text":"name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\nA unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.
URI: nmdc:sample_link
"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":"Range: String
Multivalued: True
Recommended: True
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n the field will link with the soil used in an incubation. The soil a plant was grown\n in links to the plant sample. An original culture sample was transferred to a new\n vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nmultivalued: true\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.
URI: nmdc:sample_shipped
"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":"Range: String
Recommended: True
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nType of sample being submitted
URI: nmdc:sample_type
"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":"Range: SampleTypeEnum
Recommended: True
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: sample_type_enum\nrecommended: true\n\nURI: nmdc:sampling_method
"},{"location":"sampling_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity no"},{"location":"sampling_method/#properties","title":"Properties","text":"name: sampling_method\ntitle: sampling method\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampling_method\ndomain_of:\n- MaterialSamplingActivity\nrange: SamplingMethodEnum\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000131
"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":"name: saturates_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nmultivalued: false\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal size in bp of all scaffolds.
URI: nmdc:scaf_bp
"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":"name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
URI: nmdc:scaf_l50
"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":"name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
URI: nmdc:scaf_l90
"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":"name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all scaffolds of that length or longer contains\n at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal size in bp of all scaffolds greater than 50 KB.
URI: nmdc:scaf_l_gt50k
"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase
URI: nmdc:scaf_logsum
"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":"name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum scaffold length.
URI: nmdc:scaf_max
"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":"name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
URI: nmdc:scaf_n50
"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":"name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n defined as the smallest number of scaffolds whose length sum makes up half of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
URI: nmdc:scaf_n90
"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":"name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of scaffolds greater than 50 KB.
URI: nmdc:scaf_n_gt50k
"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence size percentage of scaffolds greater than 50 KB.
URI: nmdc:scaf_pct_gt50k
"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:scaf_powsum
"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":"name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of all scaffolds.
URI: nmdc:scaffolds
"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":"name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThis document assumes knowledge of JSON. It also assumes rudimentary familiarity with JSON-Schema but don't worry if you are not an expert on this.
We can conceive of validation of a piece of JSON at two levels
It is crucial that the JSON is syntactically valid, otherwise it can't even be schema-validated.
There are a variety of ways to check for this. We recommend using jsonschema to validate this, see below.
NOTE: all NMDC JSON-producing tools, libraries, or scripts SHOULD use a standard json library. If you are using a robust standard json library, your output is practically guaranteed to be syntactically valid JSON.
It is strongly recommended that you do NOT generate JSON by methods such as directly manipulating json strings or printing directly. This is guaranteed to be fragile/non-robust. Even if your code works now, it is certain it will fail later and produce incorrect JSON.
For Python, there is only one choice:
https://docs.python.org/3/library/json.html
If you are not using this, you should
"},{"location":"schema-validation/#schema-validation","title":"Schema validation","text":"The JSON-Schema for NMDC is maintained in this github repo, under jsonschema/nmdc.schema.json
Note that the JSON-Schema is generated from a higher level YAML representation, using a modeling framework called linkML. See the README for details. For understanding the schema, you may be better looking at the auto-generated docs. However, for computational conformance, the JSON-Schema is what should be used.
There are a variety of json schema validators, these will give the same results. There are web playgrounds for this. But for simplicity we recommend the Python jsonschema package
To install:
pip install jsonschema\nAssume you have a file MYFILE that is json intended to conform
jsonschema -i /PATH/TO/MYFILE.json jsonschema/nmdc.schema.json\nIf the json is valid, there will be no output and the script will pass. If there are problems these will be reported.
You can try this with some ready-made examples in this repo:
jsonschema -i examples/nmdc-01.json jsonschema/nmdc.schema.json\nNote: nmdc.schema.json describes each model object, its required attributes and attribute types. The examples themselves use JSON notation to allow multiple instances of the objects in the JSON schema, to be submitted in one file.
You can also use the jsonschema library to validate directly from within your python.
"},{"location":"schema-validation/#what-to-do-if-your-json-does-not-validate","title":"What to do if your JSON does not validate","text":"There are 3 possibilities:
For 1, you can go right ahead and make PR on the schema yaml. However, if you are not comfortable doing this then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue.
For 2, this is upon you to fix this, however debugging can be aided in pulling out single instances of your model objects, and verifying that you are creating valid JSON (ie: paste one instance of your object into https://jsonlint.com/ or tools like it to verify its syntax). Another common issue is that you might have incorrect syntax for grouping many instances of a JSON object into an array. Using a small subsample of your data and an online linter as above, can aide in debugging this. Sometimes the validation can complain about invalid syntax if the attribute of an instance object disagrees with the schema's typing (ie: you have an integer where a string is expected).
"},{"location":"schema-validation/#nmdc-producer-sop","title":"NMDC Producer SOP","text":"It is expected that different providers of JSON within the NMDC take responsibility for validating their JSON. Aim1 can help with any problems.
Currently not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In future we would like to move towards a situation where all information is provided as JSON.
"},{"location":"season/","title":"Slot: season","text":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
URI: MIXS:0000829
"},{"location":"season/#inheritance","title":"Inheritance","text":"name: season\nannotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms listed\n under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nmultivalued: false\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\n\nTreatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment
URI: MIXS:0001068
"},{"location":"season_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: season_environment\nannotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nmultivalued: true\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000645
"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":"name: season_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nmultivalued: false\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMean seasonal temperature
URI: MIXS:0000643
"},{"location":"season_temp/#inheritance","title":"Inheritance","text":"name: season_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nmultivalued: false\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe seasons the space is occupied
URI: MIXS:0000830
"},{"location":"season_use/#inheritance","title":"Inheritance","text":"name: season_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nmultivalued: false\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\n\nThe process for substantially degrading the biological content of the sewage
URI: MIXS:0000351
"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":"name: secondary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process for substantially degrading the biological content of the\n sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nmultivalued: false\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about the sediment type based on major constituents
URI: MIXS:0001078
"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":"name: sediment_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nmultivalued: false\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\n\nSequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
URI: MIXS:0000050
"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":"name: seq_meth\nannotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nmultivalued: false\nalias: seq_meth\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nIndicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA
URI: MIXS:0000051
"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":"name: seq_quality_check\nannotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nmultivalued: false\nalias: seq_quality_check\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nThe ID of the landmark used to establish the coordinate system for the current feature.
URI: nmdc:seqid
"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":"name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\nURI: nmdc:sequencing_field
"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":"name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\nType of wastewater treatment plant as municipial or industrial
URI: MIXS:0000215
"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":"name: sewage_type\nannotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nmultivalued: false\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nSigns of the presence of mold or mildew on the shading device
URI: MIXS:0000834
"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":"name: shad_dev_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nmultivalued: false\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\n\nThe physical condition of the shading device at the time of sampling
URI: MIXS:0000831
"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":"name: shading_device_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nmultivalued: false\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\n\nThe location of the shading device in relation to the built structure
URI: MIXS:0000832
"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":"name: shading_device_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nmultivalued: false\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe material the shading device is composed of
URI: MIXS:0000245
"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":"name: shading_device_mat\nannotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nmultivalued: false\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of shading device
URI: MIXS:0000835
"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":"name: shading_device_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nmultivalued: false\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\n\nCollection design of pooled samples and/or sieve size and amount of sample sieved
URI: MIXS:0000322
"},{"location":"sieving/#inheritance","title":"Inheritance","text":"name: sieving\nannotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nmultivalued: false\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of silicate
URI: MIXS:0000184
"},{"location":"silicate/#inheritance","title":"Inheritance","text":"name: silicate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nmultivalued: false\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nFiltering pore size used in sample preparation
URI: MIXS:0000017
"},{"location":"size_frac/#inheritance","title":"Inheritance","text":"name: size_frac\nannotations:\n expected_value:\n tag: expected_value\n value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nmultivalued: false\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\n\nRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
URI: MIXS:0000735
"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":"name: size_frac_low\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nmultivalued: false\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
URI: MIXS:0000736
"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":"name: size_frac_up\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nmultivalued: false\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
URI: MIXS:0000647
"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":"name: slope_aspect\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n This measure provides an indication of sun and wind exposure that will influence\n soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nmultivalued: false\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCommonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
URI: MIXS:0000646
"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":"name: slope_gradient\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This measure\n is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nmultivalued: false\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe time activated sludge remains in reactor
URI: MIXS:0000669
"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":"name: sludge_retent_time\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nmultivalued: false\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:smarts_string
"},{"location":"smarts_string/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"smarts_string/#properties","title":"Properties","text":"name: smarts_string\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smarts_string\ndomain_of:\n- Reaction\nrange: string\n\nA string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
URI: nmdc:smiles
"},{"location":"smiles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"smiles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: smiles\ndomain_of:\n- ChemicalEntity\nrange: string\n\nSodium concentration in the sample
URI: MIXS:0000428
"},{"location":"sodium/#inheritance","title":"Inheritance","text":"name: sodium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nmultivalued: false\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:soil_annual_season_temp
"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":"name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\nSpecific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath
URI: MIXS:0001082
"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":"name: soil_horizon\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nmultivalued: false\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\n\nThe relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
URI: MIXS:0000335
"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":"name: soil_text_measure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nmultivalued: false\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining soil texture
URI: MIXS:0000336
"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":"name: soil_texture_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nmultivalued: false\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\n\nDescription of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.
URI: MIXS:0000332
"},{"location":"soil_type/#inheritance","title":"Inheritance","text":"name: soil_type\nannotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be\n separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nmultivalued: false\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in determining soil series name or other lower-level classification
URI: MIXS:0000334
"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":"name: soil_type_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nmultivalued: false\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe amount of solar energy that arrives at a specific area of a surface during a specific time interval
URI: MIXS:0000112
"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":"name: solar_irradiance\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nmultivalued: false\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
URI: MIXS:0000672
"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_inorg_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nmultivalued: true\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:soluble_iron_micromol
"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":"name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.
URI: MIXS:0000673
"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_org_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nmultivalued: true\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of soluble reactive phosphorus
URI: MIXS:0000738
"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":"name: soluble_react_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nmultivalued: false\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
URI: MIXS:0000026
"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":"name: source_mat_id\nannotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n and as opposed to a particular digital record of a material sample) used for extracting\n nucleic acids, and subsequent sequencing. The identifier can refer either to the\n original material collected or to any derived sub-samples. The INSDC qualifiers\n /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n voucher and sampled tissue with the same identifier. However, the /culture_collection\n qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n would refer to an identifier from some derived culture from which the nucleic acids\n were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nmultivalued: false\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nCustomary or normal state of the space
URI: MIXS:0000770
"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":"name: space_typ_state\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nmultivalued: false\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
URI: MIXS:0000836
"},{"location":"specific/#inheritance","title":"Inheritance","text":"name: specific\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nmultivalued: false\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\n\nSpecific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.
URI: nmdc:specific_ecosystem
"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":"name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nThe mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.
URI: MIXS:0000214
"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":"name: specific_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nmultivalued: false\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSource rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000996
"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":"name: sr_dep_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nmultivalued: false\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\n\nGeological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period(geology)). If \"other\" is specified, please propose entry in \"additional info\" field_
URI: MIXS:0000997
"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":"name: sr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nmultivalued: false\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\n\nOrigin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000994
"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":"name: sr_kerog_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nmultivalued: false\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\n\nLithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000995
"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":"name: sr_lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nmultivalued: false\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\n\nTreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0001069
"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: standing_water_regm\nannotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n span, types can be flood water or standing water, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nmultivalued: true\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe start of the feature in positive 1-based integer coordinates
URI: nmdc:start
"},{"location":"start/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was started
URI: nmdc:start_date
"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PlannedProcess no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"start_date/#properties","title":"Properties","text":"name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nDate the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_date_inc
"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_time_inc
"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:started_at_time
"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"started_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- Activity\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nURI: nmdc:status
"},{"location":"status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QualityControlReport no"},{"location":"status/#properties","title":"Properties","text":"name: status\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: status\ndomain_of:\n- QualityControlReport\nrange: StatusEnum\n\nfrom reaction participant class
URI: nmdc:stoichiometry
"},{"location":"stoichiometry/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionParticipant Instances of this link a reaction to a chemical entity participant no"},{"location":"stoichiometry/#properties","title":"Properties","text":"name: stoichiometry\ndescription: from reaction participant class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stoichiometry\ndomain_of:\n- ReactionParticipant\nrange: integer\n\nExplain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).
URI: MIXS:0000327
"},{"location":"store_cond/#inheritance","title":"Inheritance","text":"name: store_cond\nannotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nmultivalued: false\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).
URI: nmdc:strand
"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":"name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n or forward strand) or '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\nThe type of research initiative
URI: nmdc:study_category
"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":"name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\n\nURI: nmdc:study_identifiers
"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: study_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nLinks a study to one or more images.
URI: nmdc:study_image
"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":"Range: ImageValue
Multivalued: True
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Study\nmultivalued: true\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\ninlined: true\n\nThis property links a database object to the set of studies within it.
URI: nmdc:study_set
"},{"location":"study_set/#inheritance","title":"Inheritance","text":"Range: Study
Multivalued: True
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: study_set\ndomain_of:\n- Database\nrange: Study\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:subject
"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no"},{"location":"subject/#properties","title":"Properties","text":"name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\nrange: GeneProduct\n\nThe substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
URI: MIXS:0000767
"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":"Range: SubstructureTypeEnum
Multivalued: True
name: substructure_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The substructure or under building is that largely hidden section of\n the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nmultivalued: true\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\n\nURI: nmdc:subsurface_depth
"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":"name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfate in the sample
URI: MIXS:0000423
"},{"location":"sulfate/#inheritance","title":"Inheritance","text":"name: sulfate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nmultivalued: false\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal sulfate concentration in the hydrocarbon resource
URI: MIXS:0000407
"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":"name: sulfate_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nmultivalued: false\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfide in the sample
URI: MIXS:0000424
"},{"location":"sulfide/#inheritance","title":"Inheritance","text":"name: sulfide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nmultivalued: false\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nContaminant identified on surface
URI: MIXS:0000759
"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":"Range: SurfAirContEnum
Multivalued: True
name: surf_air_cont\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nmultivalued: true\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\n\nSurfaces: water activity as a function of air and material moisture
URI: MIXS:0000123
"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":"name: surf_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nmultivalued: false\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSurface materials at the point of sampling
URI: MIXS:0000758
"},{"location":"surf_material/#inheritance","title":"Inheritance","text":"name: surf_material\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nmultivalued: false\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\n\nWater held on a surface
URI: MIXS:0000128
"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":"name: surf_moisture\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nmultivalued: false\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nph measurement of surface
URI: MIXS:0000760
"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":"name: surf_moisture_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nmultivalued: false\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\n\nTemperature of the surface at the time of sampling
URI: MIXS:0000125
"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":"name: surf_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nmultivalued: false\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of suspended particulate matter
URI: MIXS:0000741
"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":"name: suspend_part_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nmultivalued: false\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
URI: MIXS:0000150
"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: suspend_solids\nannotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances including a wide variety of material, such\n as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nmultivalued: true\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)
URI: MIXS:0000120
"},{"location":"tan/#inheritance","title":"Inheritance","text":"name: tan\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nmultivalued: false\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTargeted gene or locus name for marker gene studies
URI: MIXS:0000044
"},{"location":"target_gene/#inheritance","title":"Inheritance","text":"name: target_gene\nannotations:\n expected_value:\n tag: expected_value\n value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nmultivalued: false\nalias: target_gene\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nName of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
URI: MIXS:0000045
"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":"name: target_subfragment\nannotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nmultivalued: false\nalias: target_subfragment\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nIf sending technical replicates of the same sample, indicate the replicate count.
URI: nmdc:technical_reps
"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":"Range: String
Recommended: True
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nTemperature of the sample at the time of sampling.
URI: MIXS:0000113
"},{"location":"temp/#inheritance","title":"Inheritance","text":"name: temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nmultivalued: false\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe recorded temperature value at sampling time outside
URI: MIXS:0000197
"},{"location":"temp_out/#inheritance","title":"Inheritance","text":"name: temp_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nmultivalued: false\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\n\npointer to an ontology class
URI: nmdc:term
"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes"},{"location":"term/#properties","title":"Properties","text":"name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: ControlledTermValue\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\nThe process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
URI: MIXS:0000352
"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":"name: tertiary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nmultivalued: false\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nStage of tide
URI: MIXS:0000750
"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":"name: tidal_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nmultivalued: false\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\n\nNote method(s) used for tilling
URI: MIXS:0001081
"},{"location":"tillage/#inheritance","title":"Inheritance","text":"Range: TillageEnum
Multivalued: True
name: tillage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nmultivalued: true\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\n\nDescription of plant tissue culture growth media used
URI: MIXS:0001070
"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":"name: tiss_cult_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nmultivalued: false\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\n\nA name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.
URI: nmdc:title
"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":"name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the GOLD\n system has assigned a name/label. However, for display purposes, we may also wish\n the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\nConcentration of toluene in the sample
URI: MIXS:0000154
"},{"location":"toluene/#inheritance","title":"Inheritance","text":"name: toluene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nmultivalued: false\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:too_short_contig_num
"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":"name: too_short_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nTotal carbon content
URI: MIXS:0000525
"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":"name: tot_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nmultivalued: false\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of total depth of water column
URI: MIXS:0000634
"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":"name: tot_depth_water_col\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nmultivalued: false\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
URI: MIXS:0000744
"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":"name: tot_diss_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nmultivalued: false\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal inorganic nitrogen content
URI: MIXS:0000745
"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":"name: tot_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nmultivalued: false\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of total iron in the sample
URI: MIXS:0000105
"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":"name: tot_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nmultivalued: false\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
URI: MIXS:0000102
"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":"name: tot_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nmultivalued: false\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining the total nitrogen
URI: MIXS:0000338
"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":"name: tot_nitro_cont_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nmultivalued: false\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\n\nTotal nitrogen content of the sample
URI: MIXS:0000530
"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":"name: tot_nitro_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nmultivalued: false\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining total organic carbon
URI: MIXS:0000337
"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":"name: tot_org_c_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nmultivalued: false\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nDefinition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
URI: MIXS:0000533
"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":"name: tot_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nmultivalued: false\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal particulate carbon content
URI: MIXS:0000747
"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":"name: tot_part_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nmultivalued: false\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
URI: MIXS:0000117
"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":"name: tot_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nmultivalued: false\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal amount or concentration of phosphate
URI: MIXS:0000689
"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":"name: tot_phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nmultivalued: false\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of total sulfur in the sample
URI: MIXS:0000419
"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":"name: tot_sulfur\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nmultivalued: false\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:total_bases
"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":"name: total_bases\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: string\n\nThe subway line name
URI: MIXS:0000837
"},{"location":"train_line/#inheritance","title":"Inheritance","text":"name: train_line\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nmultivalued: false\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\n\nThe train station collection location
URI: MIXS:0000838
"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":"name: train_stat_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nmultivalued: false\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\n\nThe train stop collection location
URI: MIXS:0000839
"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":"name: train_stop_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nmultivalued: false\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\n\nMeasure of the amount of cloudiness or haziness in water caused by individual particles
URI: MIXS:0000191
"},{"location":"turbidity/#inheritance","title":"Inheritance","text":"name: turbidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nmultivalued: false\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).
URI: MIXS:0000397
"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nmultivalued: false\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).
URI: MIXS:0000394
"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nmultivalued: false\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCustomary or normal density of occupants
URI: MIXS:0000771
"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":"name: typ_occup_density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nmultivalued: false\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\n\nAn optional string that specifies the type object. This is used to allow for searches for different kinds of objects.
URI: nmdc:type
"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no CreditAssociation This class supports binding associated researchers to studies no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MagBin no GenomeFeature A feature localized to an interval along a genome yes MetatranscriptomeAssembly no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"type/#properties","title":"Properties","text":"name: type\ndescription: An optional string that specifies the type object. This is used to allow\n for searches for different kinds of objects.\ndeprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: type\ndomain_of:\n- DataObject\n- Biosample\n- Study\n- OmicsProcessing\n- CreditAssociation\n- WorkflowExecutionActivity\n- MetagenomeAssembly\n- MetagenomeAnnotationActivity\n- MetatranscriptomeAnnotationActivity\n- MetatranscriptomeActivity\n- MagsAnalysisActivity\n- ReadQcAnalysisActivity\n- ReadBasedTaxonomyAnalysisActivity\n- MagBin\n- GenomeFeature\nrange: string\n\nLast generated 2023-01-12
If a class doesn't use the id slot, then there is no need to assign that class a typecode
Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of its ancestors. This table does not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' for WorkflowExecutionActivity, which is inherited from it's ancestor Activity
Todo:
URI: nmdc:unbinned_contig_num
"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":"name: unbinned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nURI: nmdc:url
"},{"location":"url/#inheritance","title":"Inheritance","text":"name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: url\ndomain_of:\n- Protocol\n- DataObject\n- ImageValue\nrange: string\n\nURI: nmdc:used
"},{"location":"used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity yes NomAnalysisActivity yes"},{"location":"used/#properties","title":"Properties","text":"name: used\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:used\nrank: 1000\ndomain: Activity\nalias: used\ndomain_of:\n- Activity\nrange: string\n\nVentilation rate of the system in the sampled premises
URI: MIXS:0000114
"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":"name: ventilation_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nmultivalued: false\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nVentilation system used in the sampled premises
URI: MIXS:0000756
"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":"name: ventilation_type\nannotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nmultivalued: false\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:version
"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"version/#properties","title":"Properties","text":"name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecutionActivity\n- ReadQcAnalysisActivity\nrange: string\n\nConcentration of Volatile Fatty Acids in the sample
URI: MIXS:0000152
"},{"location":"vfa/#inheritance","title":"Inheritance","text":"name: vfa\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nmultivalued: false\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal volatile fatty acid concentration in the hydrocarbon resource
URI: MIXS:0000408
"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":"name: vfa_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nmultivalued: false\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building visual media
URI: MIXS:0000840
"},{"location":"vis_media/#inheritance","title":"Inheritance","text":"name: vis_media\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nmultivalued: false\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\n\nA measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)
URI: MIXS:0000126
"},{"location":"viscosity/#inheritance","title":"Inheritance","text":"name: viscosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nmultivalued: false\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
URI: MIXS:0000115
"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: volatile_org_comp\nannotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n temperature; can report multiple volatile organic compounds by entering numeric\n values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nmultivalued: true\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total area of the sampled room's walls
URI: MIXS:0000198
"},{"location":"wall_area/#inheritance","title":"Inheritance","text":"name: wall_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nmultivalued: false\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building class of the wall defined by the composition of the building elements and fire-resistance rating.
URI: MIXS:0000841
"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":"name: wall_const_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building class of the wall defined by the composition of the building\n elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nmultivalued: false\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\n\nThe material utilized to finish the outer most layer of the wall
URI: MIXS:0000842
"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":"name: wall_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nmultivalued: false\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\n\nThe average height of the walls in the sampled room
URI: MIXS:0000221
"},{"location":"wall_height/#inheritance","title":"Inheritance","text":"name: wall_height\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nmultivalued: false\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe relative location of the wall within the room
URI: MIXS:0000843
"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":"name: wall_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nmultivalued: false\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\n\nThe surface treatment of interior wall
URI: MIXS:0000845
"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":"name: wall_surf_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nmultivalued: false\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\n\nThe feel, appearance, or consistency of a wall surface
URI: MIXS:0000846
"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":"name: wall_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nmultivalued: false\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\n\nThe ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
URI: MIXS:0000222
"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":"name: wall_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nmultivalued: false\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSigns of the presence of mold or mildew on a wall
URI: MIXS:0000844
"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":"name: wall_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nmultivalued: false\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:was_generated_by
"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no AttributeValue The value for any value of a attribute for a sample no FunctionalAnnotation An assignment of a function term (e yes InstrumentValue no QuantityValue A simple quantity, e no ImageValue An attribute value representing an image no PersonValue An attribute value representing a person no TextValue A basic string value no UrlValue A value that is a string that conforms to URL syntax no TimestampValue A value that is a timestamp no IntegerValue A value that is an integer no BooleanValue A value that is a boolean no ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no GeolocationValue A normalized value for a location on the earth's surface no"},{"location":"was_generated_by/#properties","title":"Properties","text":"name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- DataObject\n- AttributeValue\n- FunctionalAnnotation\nrange: Activity\n\nURI: nmdc:was_informed_by
"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"was_informed_by/#properties","title":"Properties","text":"name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- Activity\nrange: Activity\n\nThe origin of wastewater such as human waste, rainfall, storm drains, etc.
URI: MIXS:0000353
"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":"name: wastewater_type\nannotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nmultivalued: false\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nReference or method used in determining the water content of soil
URI: MIXS:0000323
"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":"name: water_cont_soil_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nmultivalued: false\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\n\nWater content measurement
URI: MIXS:0000185
"},{"location":"water_content/#inheritance","title":"Inheritance","text":"name: water_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nmultivalued: false\nalias: water_content\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of magnitude and direction of flow within a fluid
URI: MIXS:0000203
"},{"location":"water_current/#inheritance","title":"Inheritance","text":"name: water_current\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nmultivalued: false\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCurrent amount of water (%) in a produced fluid stream; or the average of the combined streams
URI: MIXS:0000454
"},{"location":"water_cut/#inheritance","title":"Inheritance","text":"name: water_cut\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nmultivalued: false\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe size of the water feature
URI: MIXS:0000223
"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":"name: water_feat_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nmultivalued: false\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of water feature present within the building being sampled
URI: MIXS:0000847
"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":"name: water_feat_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nmultivalued: false\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\n\nWater production rates per well (e.g. 987 m3 / day)
URI: MIXS:0000453
"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":"name: water_prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nmultivalued: false\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000590
"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: water_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nmultivalued: true\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000591
"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: watering_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can include\n multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nmultivalued: true\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nA list of websites that are associated with the entity.
URI: nmdc:websites
"},{"location":"websites/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes PersonValue An attribute value representing a person no"},{"location":"websites/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: websites\ndescription: A list of websites that are associated with the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: websites\ndomain_of:\n- Study\n- PersonValue\nrange: string\n\nThe day of the week when sampling occurred
URI: MIXS:0000848
"},{"location":"weekday/#inheritance","title":"Inheritance","text":"name: weekday\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nmultivalued: false\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\n\nA unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)
URI: MIXS:0000297
"},{"location":"win/#inheritance","title":"Inheritance","text":"name: win\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nmultivalued: false\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\n\nWind direction is the direction from which a wind originates
URI: MIXS:0000757
"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":"name: wind_direction\nannotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nmultivalued: false\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\n\nSpeed of wind measured at the time of sampling
URI: MIXS:0000118
"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":"name: wind_speed\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nmultivalued: false\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the window at the time of sampling
URI: MIXS:0000849
"},{"location":"window_cond/#inheritance","title":"Inheritance","text":"name: window_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nmultivalued: false\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\n\nThe type of window covering
URI: MIXS:0000850
"},{"location":"window_cover/#inheritance","title":"Inheritance","text":"name: window_cover\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nmultivalued: false\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\n\nThe horizontal position of the window on the wall
URI: MIXS:0000851
"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":"name: window_horiz_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nmultivalued: false\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\n\nThe relative location of the window within the room
URI: MIXS:0000852
"},{"location":"window_loc/#inheritance","title":"Inheritance","text":"name: window_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nmultivalued: false\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\n\nThe type of material used to finish a window
URI: MIXS:0000853
"},{"location":"window_mat/#inheritance","title":"Inheritance","text":"name: window_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nmultivalued: false\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\n\nThe number of times windows are opened per week
URI: MIXS:0000246
"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":"name: window_open_freq\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nmultivalued: false\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe window's length and width
URI: MIXS:0000224
"},{"location":"window_size/#inheritance","title":"Inheritance","text":"name: window_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nmultivalued: false\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\n\nDefines whether the windows were open or closed during environmental testing
URI: MIXS:0000855
"},{"location":"window_status/#inheritance","title":"Inheritance","text":"name: window_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nmultivalued: false\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of windows
URI: MIXS:0000856
"},{"location":"window_type/#inheritance","title":"Inheritance","text":"name: window_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nmultivalued: false\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\n\nThe vertical position of the window on the wall
URI: MIXS:0000857
"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":"name: window_vert_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nmultivalued: false\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\n\nSigns of the presence of mold or mildew on the window.
URI: MIXS:0000854
"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":"name: window_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nmultivalued: false\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of xylene in the sample
URI: MIXS:0000156
"},{"location":"xylene/#inheritance","title":"Inheritance","text":"name: xylene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nmultivalued: false\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of zinc in the sample
URI: nmdc:zinc
"},{"location":"zinc/#inheritance","title":"Inheritance","text":"name: zinc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nis_a: attribute\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSchema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:
URI: https://w3id.org/nmdc/nmdc
"},{"location":"#classes","title":"Classes","text":"Class Description Activity a provence-generating activity WorkflowExecutionActivity Represents an instance of an execution of a particular workflow MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysisActivity MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis MetaproteomicsAnalysisActivity MetatranscriptomeActivity A metatranscriptome activity that e MetatranscriptomeAnnotationActivity MetatranscriptomeAssembly NomAnalysisActivity ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... AttributeValue The value for any value of a attribute for a sample BooleanValue A value that is a boolean ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image InstrumentValue IntegerValue A value that is an integer PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp UrlValue A value that is a string that conforms to URL syntax CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data DissolvingActivity FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome LabDevice MagBin MaterialContainer MaterialSamplingActivity MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... NamedThing a databased entity or concept/class DataObject An object that primarily consists of symbols that represent information GeneProduct A molecule encoded by a gene that has an evolved function Instrument A material entity that is designed to perform a function in a scientific inve... MaterialEntity AnalyticalSample Biosample Biological source material which can be characterized by an experiment ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected MaterialSample OntologyClass ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... Reaction An individual biochemical transformation carried out by a functional unit of ... PlannedProcess BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... Extraction A material separation in which a desired component of an input material is se... LibraryPreparation Pooling physical combination of several instances of like material CollectingBiosamplesFromSite OmicsProcessing The methods and processes used to generate omics data from a biosample or org... Study A study summarizes the overall goal of a research initiative and outlines the... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol QualityControlReport ReactionActivity ReactionParticipant Instances of this link a reaction to a chemical entity participant"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture activity_set This property links a database object to the set of workflow activities activity_speed activity_temperature activity_time add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternate_emails One or more other email addresses for an entity alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_collected amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_role applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers atmospheric_data Measurement of atmospheric data; can include multiple data attribute A attribute of a biosample avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... award_dois One or more DOIs that links a study, or similar entiry, to information about ... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name bin_quality binned_contig_num biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... calcium Concentration of calcium in the sample canary a slot that can be added and removed as evidence that schema changes have pro... carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical from reaction participant class chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collected_into collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness completion_date compression_type If provided, specifies the compression type conduc Electrical conductivity of water container_size container_type contamination contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object dataset_dois One or more DOIs that links a study, or similar entity, to the generated data date_created from database class date_last_rain The date of the last time it rained density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing device_type dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids direction One of l->r, r->l, bidirectional, neutral display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dissolution_aided_by dissolution_reagent dissolution_volume dissolved_in dissolving_activity_set dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna dois A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_dois One or more DOIs that links to an EMSL Research Campaign page emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ess_dive_datasets List of ESS-DIVE dataset DOIs ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class execution_resource exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_method extraction_set This property links a database object to the set of extractions within it extraction_target extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_method Type of filter used or how the sample was filtered filter_type A device which removes solid particulates or airborne molecular contaminants fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count gene_function_id genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis project in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class gtdbtk_domain gtdbtk_family gtdbtk_genus gtdbtk_order gtdbtk_phylum gtdbtk_species habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_numeric_value has_raw_value has_unit Example \"m\" has_boolean_value Links a quantity value to a boolean has_calibration A reference to a file that holds calibration information has_credit_associations This slot links a study to a credit association has_function has_input An input to a process has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_quantifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output biosample to a processing step has_part A pathway can be broken down to a series of reaction step has_participants has_peptide_quantifications has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_name The name of the instrument that was used for processing the sample int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... investigation_field field describing aspect of the investigation/study to which the sample belong... is_balanced is_diastereoselective is_fully_characterized False if includes R-groups is_stereo is_transport isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... keywords A list of keywords that used to associate the entity language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation left_participants library_preparation_kit library_preparation_set This property links a database object to the set of DNA extractions within it library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num magnesium Concentration of magnesium in the sample mags_activity_set This property links a database object to the set of MAGs analysis activities mags_list manganese Concentration of manganese in the sample massive_identifiers identifiers for entities according to MASSIVE massive_study_identifiers identifiers for corresponding study in MASSIVE material_input material_output material_sample_set material_sampling_activity_set max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id metabolite_quantified the specific metabolite identifier metabolomics_analysis_activity_set This property links a database object to the set of metabolomics analysis act... metagenome_annotation_activity_set This property links a database object to the set of metagenome annotation act... metagenome_annotation_id metagenome_assembly_parameter metagenome_assembly_set This property links a database object to the set of metagenome assembly activ... metagenome_sequencing_activity_set This property links a database object to the set of metagenome sequencing act... metaproteomics_analysis_activity_set This property links a database object to the set of metaproteomics analysis a... metatranscriptome_activity_set This property links a database object to the set of metatranscriptome analysi... methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_deims_sdr_link neon_eco_type neon_identifiers identifiers for entities according to NEON neon_soil_type neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) nom_analysis_activity_set This property links a database object to the set of natural organic matter (N... non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes from study class nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field nucleic_acid_concentration num_16s num_23s num_5s num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna number_of_contig number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_processing_set This property links a database object to the set of omics processings within ... omics_type The type of omics data orcid The ORCID of a person org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed pooling_set porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_link publication_dois One or more DOIs that links a study, or similar entity, to a publication publications A list of publications that are associated with the entity quad_pos The quadrant position of the sampling room within the building quality_control_report radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reaction_activity_set reaction_aided_by reaction_temperature reaction_time reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_based_taxonomy_analysis_activity_set This property links a database object to the set of read based analysis activ... read_qc_analysis_activity_set This property links a database object to the set of read QC analysis activiti... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... relevant_protocols replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... right_participants rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_type Type of sample being submitted sampling_method saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smarts_string smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time status stoichiometry from reaction participant class store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type An optional string that specifies the type object unbinned_contig_num url used ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum ArchStrucEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ContainerTypeEnum CreditEnum CurLandUseEnum DeposEnvEnum DeviceTypeEnum DnaSampleFormatEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum IntWallCondEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum MechStrucEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum ProcessingInstitutionEnum ProfilePositionEnum QuadPosEnum RelSampLocEnum RnaSampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SampleTypeEnum SamplingMethodEnum SeasonUseEnum SedimentTypeEnum ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SolventEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StatusEnum StudyCategoryEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description Checklist A MIxS checklist ChecklistPackageCombination A combination of a checklist and a package DataObjectSubset Subset consisting of the data objects that either inputs or outputs of proces... Environment Investigation MixsExtension MixsEnvironmentalTriad NucleicAcidSequenceSource Package A MIxS package SampleSubset Subset consisting of entities linked to the processing of samples Sequencing WorkflowSubset Subset consisting of just the workflow execution activities"},{"location":"Activity/","title":"Class: Activity","text":"a provence-generating activity
URI: nmdc:Activity
classDiagram\n class Activity\n Activity <|-- WorkflowExecutionActivity\n\n Activity : ended_at_time\n\n Activity : id\n\n Activity : name\n\n Activity : started_at_time\n\n Activity : used\n\n Activity : was_informed_by\n\n Activity --|> Activity : was_informed_by\n\n\nname: Activity\ndescription: a provence-generating activity\nnotes:\n- removed was_associated_with because we are trying to avoid instantiating id-less\n Agents\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:Activity\nslots:\n- id\n- name\n- started_at_time\n- ended_at_time\n- was_informed_by\n- used\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Activity\ndescription: a provence-generating activity\nnotes:\n- removed was_associated_with because we are trying to avoid instantiating id-less\n Agents\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:Activity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Activity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:act-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Activity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: Activity\n domain_of:\n - Activity\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: Activity\n domain_of:\n - Activity\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: Activity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: Activity\n domain_of:\n - Activity\n range: string\n\nURI: AnalysisTypeEnum
"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None metaproteomics None metatranscriptomics None natural organic matter None"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":"name: analysis_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metabolomics:\n text: metabolomics\n metagenomics:\n text: metagenomics\n metaproteomics:\n text: metaproteomics\n metatranscriptomics:\n text: metatranscriptomics\n natural organic matter:\n text: natural organic matter\n\nURI: nmdc:AnalyticalSample
classDiagram\n class AnalyticalSample\n MaterialEntity <|-- AnalyticalSample\n\n AnalyticalSample : alternative_identifiers\n\n AnalyticalSample : description\n\n AnalyticalSample : id\n\n AnalyticalSample : name\n\n\nname: AnalyticalSample\ntitle: Analytical Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: AnalyticalSample\ntitle: Analytical Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: AnalyticalSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:ansm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: AnalyticalSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: AnalyticalSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: AnalyticalSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ArchStrucEnum
"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":"name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building:\n text: building\n shed:\n text: shed\n home:\n text: home\n\nThe value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value
URI: nmdc:AttributeValue
classDiagram\n class AttributeValue\n AttributeValue <|-- InstrumentValue\n AttributeValue <|-- QuantityValue\n AttributeValue <|-- ImageValue\n AttributeValue <|-- PersonValue\n AttributeValue <|-- TextValue\n AttributeValue <|-- UrlValue\n AttributeValue <|-- TimestampValue\n AttributeValue <|-- IntegerValue\n AttributeValue <|-- BooleanValue\n AttributeValue <|-- ControlledTermValue\n AttributeValue <|-- GeolocationValue\n\n AttributeValue : has_raw_value\n\n AttributeValue : was_generated_by\n\n AttributeValue --|> Activity : was_generated_by\n\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- has_raw_value\n- was_generated_by\nslot_usage:\n type:\n name: type\n description: An optional string that specified the type of object.\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n type:\n name: type\n description: An optional string that specified the type of object.\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: AttributeValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: AttributeValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: BiolStatEnum
"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":"name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n wild:\n text: wild\n natural:\n text: natural\n semi-natural:\n text: semi-natural\n inbred line:\n text: inbred line\n breeder's line:\n text: breeder's line\n hybrid:\n text: hybrid\n clonal selection:\n text: clonal selection\n mutant:\n text: mutant\n\nBiological source material which can be characterized by an experiment.
URI: nmdc:Biosample
classDiagram\n class Biosample\n MaterialEntity <|-- Biosample\n\n Biosample : abs_air_humidity\n\n Biosample --|> QuantityValue : abs_air_humidity\n\n Biosample : add_date\n\n Biosample : add_recov_method\n\n Biosample --|> TextValue : add_recov_method\n\n Biosample : additional_info\n\n Biosample --|> TextValue : additional_info\n\n Biosample : address\n\n Biosample --|> TextValue : address\n\n Biosample : adj_room\n\n Biosample --|> TextValue : adj_room\n\n Biosample : aero_struc\n\n Biosample --|> TextValue : aero_struc\n\n Biosample : agrochem_addition\n\n Biosample --|> TextValue : agrochem_addition\n\n Biosample : air_PM_concen\n\n Biosample --|> TextValue : air_PM_concen\n\n Biosample : air_temp\n\n Biosample --|> QuantityValue : air_temp\n\n Biosample : air_temp_regm\n\n Biosample --|> TextValue : air_temp_regm\n\n Biosample : al_sat\n\n Biosample --|> QuantityValue : al_sat\n\n Biosample : al_sat_meth\n\n Biosample --|> TextValue : al_sat_meth\n\n Biosample : alkalinity\n\n Biosample --|> QuantityValue : alkalinity\n\n Biosample : alkalinity_method\n\n Biosample --|> TextValue : alkalinity_method\n\n Biosample : alkyl_diethers\n\n Biosample --|> QuantityValue : alkyl_diethers\n\n Biosample : alt\n\n Biosample --|> QuantityValue : alt\n\n Biosample : alternative_identifiers\n\n Biosample : aminopept_act\n\n Biosample --|> QuantityValue : aminopept_act\n\n Biosample : ammonium\n\n Biosample --|> QuantityValue : ammonium\n\n Biosample : ammonium_nitrogen\n\n Biosample --|> QuantityValue : ammonium_nitrogen\n\n Biosample : amount_light\n\n Biosample --|> QuantityValue : amount_light\n\n Biosample : analysis_type\n\n Biosample --|> analysis_type_enum : analysis_type\n\n Biosample : ances_data\n\n Biosample --|> TextValue : ances_data\n\n Biosample : annual_precpt\n\n Biosample --|> QuantityValue : annual_precpt\n\n Biosample : annual_temp\n\n Biosample --|> QuantityValue : annual_temp\n\n Biosample : antibiotic_regm\n\n Biosample --|> TextValue : antibiotic_regm\n\n Biosample : api\n\n Biosample --|> QuantityValue : api\n\n Biosample : arch_struc\n\n Biosample --|> arch_struc_enum : arch_struc\n\n Biosample : aromatics_pc\n\n Biosample --|> TextValue : aromatics_pc\n\n Biosample : asphaltenes_pc\n\n Biosample --|> TextValue : asphaltenes_pc\n\n Biosample : atmospheric_data\n\n Biosample --|> TextValue : atmospheric_data\n\n Biosample : avg_dew_point\n\n Biosample --|> QuantityValue : avg_dew_point\n\n Biosample : avg_occup\n\n Biosample --|> TextValue : avg_occup\n\n Biosample : avg_temp\n\n Biosample --|> QuantityValue : avg_temp\n\n Biosample : bac_prod\n\n Biosample --|> QuantityValue : bac_prod\n\n Biosample : bac_resp\n\n Biosample --|> QuantityValue : bac_resp\n\n Biosample : bacteria_carb_prod\n\n Biosample --|> QuantityValue : bacteria_carb_prod\n\n Biosample : barometric_press\n\n Biosample --|> QuantityValue : barometric_press\n\n Biosample : basin\n\n Biosample --|> TextValue : basin\n\n Biosample : bathroom_count\n\n Biosample --|> TextValue : bathroom_count\n\n Biosample : bedroom_count\n\n Biosample --|> TextValue : bedroom_count\n\n Biosample : benzene\n\n Biosample --|> QuantityValue : benzene\n\n Biosample : biochem_oxygen_dem\n\n Biosample --|> QuantityValue : biochem_oxygen_dem\n\n Biosample : biocide\n\n Biosample --|> TextValue : biocide\n\n Biosample : biocide_admin_method\n\n Biosample --|> TextValue : biocide_admin_method\n\n Biosample : biol_stat\n\n Biosample --|> biol_stat_enum : biol_stat\n\n Biosample : biomass\n\n Biosample --|> TextValue : biomass\n\n Biosample : biosample_categories\n\n Biosample --|> BiosampleCategoryEnum : biosample_categories\n\n Biosample : biotic_regm\n\n Biosample --|> TextValue : biotic_regm\n\n Biosample : biotic_relationship\n\n Biosample --|> biotic_relationship_enum : biotic_relationship\n\n Biosample : bishomohopanol\n\n Biosample --|> QuantityValue : bishomohopanol\n\n Biosample : blood_press_diast\n\n Biosample --|> QuantityValue : blood_press_diast\n\n Biosample : blood_press_syst\n\n Biosample --|> QuantityValue : blood_press_syst\n\n Biosample : bromide\n\n Biosample --|> QuantityValue : bromide\n\n Biosample : build_docs\n\n Biosample --|> build_docs_enum : build_docs\n\n Biosample : build_occup_type\n\n Biosample --|> build_occup_type_enum : build_occup_type\n\n Biosample : building_setting\n\n Biosample --|> building_setting_enum : building_setting\n\n Biosample : built_struc_age\n\n Biosample --|> QuantityValue : built_struc_age\n\n Biosample : built_struc_set\n\n Biosample --|> TextValue : built_struc_set\n\n Biosample : built_struc_type\n\n Biosample --|> TextValue : built_struc_type\n\n Biosample : calcium\n\n Biosample --|> QuantityValue : calcium\n\n Biosample : carb_dioxide\n\n Biosample --|> QuantityValue : carb_dioxide\n\n Biosample : carb_monoxide\n\n Biosample --|> QuantityValue : carb_monoxide\n\n Biosample : carb_nitro_ratio\n\n Biosample --|> QuantityValue : carb_nitro_ratio\n\n Biosample : ceil_area\n\n Biosample --|> QuantityValue : ceil_area\n\n Biosample : ceil_cond\n\n Biosample --|> ceil_cond_enum : ceil_cond\n\n Biosample : ceil_finish_mat\n\n Biosample --|> ceil_finish_mat_enum : ceil_finish_mat\n\n Biosample : ceil_struc\n\n Biosample --|> TextValue : ceil_struc\n\n Biosample : ceil_texture\n\n Biosample --|> ceil_texture_enum : ceil_texture\n\n Biosample : ceil_thermal_mass\n\n Biosample --|> QuantityValue : ceil_thermal_mass\n\n Biosample : ceil_type\n\n Biosample --|> ceil_type_enum : ceil_type\n\n Biosample : ceil_water_mold\n\n Biosample --|> TextValue : ceil_water_mold\n\n Biosample : chem_administration\n\n Biosample --|> ControlledTermValue : chem_administration\n\n Biosample : chem_mutagen\n\n Biosample --|> TextValue : chem_mutagen\n\n Biosample : chem_oxygen_dem\n\n Biosample --|> QuantityValue : chem_oxygen_dem\n\n Biosample : chem_treat_method\n\n Biosample : chem_treatment\n\n Biosample --|> TextValue : chem_treatment\n\n Biosample : chimera_check\n\n Biosample --|> TextValue : chimera_check\n\n Biosample : chloride\n\n Biosample --|> QuantityValue : chloride\n\n Biosample : chlorophyll\n\n Biosample --|> QuantityValue : chlorophyll\n\n Biosample : climate_environment\n\n Biosample --|> TextValue : climate_environment\n\n Biosample : collected_from\n\n Biosample --|> FieldResearchSite : collected_from\n\n Biosample : collection_date\n\n Biosample --|> TimestampValue : collection_date\n\n Biosample : collection_date_inc\n\n Biosample : collection_time\n\n Biosample : collection_time_inc\n\n Biosample : community\n\n Biosample : conduc\n\n Biosample --|> QuantityValue : conduc\n\n Biosample : cool_syst_id\n\n Biosample --|> TextValue : cool_syst_id\n\n Biosample : core_field\n\n Biosample : crop_rotation\n\n Biosample --|> TextValue : crop_rotation\n\n Biosample : cult_root_med\n\n Biosample --|> TextValue : cult_root_med\n\n Biosample : cur_land_use\n\n Biosample --|> cur_land_use_enum : cur_land_use\n\n Biosample : cur_vegetation\n\n Biosample --|> TextValue : cur_vegetation\n\n Biosample : cur_vegetation_meth\n\n Biosample --|> TextValue : cur_vegetation_meth\n\n Biosample : date_last_rain\n\n Biosample --|> TimestampValue : date_last_rain\n\n Biosample : density\n\n Biosample --|> QuantityValue : density\n\n Biosample : depos_env\n\n Biosample --|> depos_env_enum : depos_env\n\n Biosample : depth\n\n Biosample --|> QuantityValue : depth\n\n Biosample : description\n\n Biosample : dew_point\n\n Biosample --|> QuantityValue : dew_point\n\n Biosample : diether_lipids\n\n Biosample --|> TextValue : diether_lipids\n\n Biosample : diss_carb_dioxide\n\n Biosample --|> QuantityValue : diss_carb_dioxide\n\n Biosample : diss_hydrogen\n\n Biosample --|> QuantityValue : diss_hydrogen\n\n Biosample : diss_inorg_carb\n\n Biosample --|> QuantityValue : diss_inorg_carb\n\n Biosample : diss_inorg_nitro\n\n Biosample --|> QuantityValue : diss_inorg_nitro\n\n Biosample : diss_inorg_phosp\n\n Biosample --|> QuantityValue : diss_inorg_phosp\n\n Biosample : diss_iron\n\n Biosample --|> QuantityValue : diss_iron\n\n Biosample : diss_org_carb\n\n Biosample --|> QuantityValue : diss_org_carb\n\n Biosample : diss_org_nitro\n\n Biosample --|> QuantityValue : diss_org_nitro\n\n Biosample : diss_oxygen\n\n Biosample --|> QuantityValue : diss_oxygen\n\n Biosample : diss_oxygen_fluid\n\n Biosample --|> QuantityValue : diss_oxygen_fluid\n\n Biosample : dna_absorb1\n\n Biosample : dna_absorb2\n\n Biosample : dna_collect_site\n\n Biosample : dna_concentration\n\n Biosample : dna_cont_type\n\n Biosample --|> JgiContTypeEnum : dna_cont_type\n\n Biosample : dna_cont_well\n\n Biosample : dna_container_id\n\n Biosample : dna_dnase\n\n Biosample --|> YesNoEnum : dna_dnase\n\n Biosample : dna_isolate_meth\n\n Biosample : dna_organisms\n\n Biosample : dna_project_contact\n\n Biosample : dna_samp_id\n\n Biosample : dna_sample_format\n\n Biosample --|> dna_sample_format_enum : dna_sample_format\n\n Biosample : dna_sample_name\n\n Biosample : dna_seq_project\n\n Biosample : dna_seq_project_name\n\n Biosample : dna_seq_project_pi\n\n Biosample : dna_volume\n\n Biosample : dnase_rna\n\n Biosample --|> YesNoEnum : dnase_rna\n\n Biosample : door_comp_type\n\n Biosample --|> door_comp_type_enum : door_comp_type\n\n Biosample : door_cond\n\n Biosample --|> door_cond_enum : door_cond\n\n Biosample : door_direct\n\n Biosample --|> door_direct_enum : door_direct\n\n Biosample : door_loc\n\n Biosample --|> door_loc_enum : door_loc\n\n Biosample : door_mat\n\n Biosample --|> door_mat_enum : door_mat\n\n Biosample : door_move\n\n Biosample --|> door_move_enum : door_move\n\n Biosample : door_size\n\n Biosample --|> QuantityValue : door_size\n\n Biosample : door_type\n\n Biosample --|> door_type_enum : door_type\n\n Biosample : door_type_metal\n\n Biosample --|> door_type_metal_enum : door_type_metal\n\n Biosample : door_type_wood\n\n Biosample --|> door_type_wood_enum : door_type_wood\n\n Biosample : door_water_mold\n\n Biosample --|> TextValue : door_water_mold\n\n Biosample : down_par\n\n Biosample --|> QuantityValue : down_par\n\n Biosample : drainage_class\n\n Biosample --|> drainage_class_enum : drainage_class\n\n Biosample : drawings\n\n Biosample --|> drawings_enum : drawings\n\n Biosample : ecosystem\n\n Biosample : ecosystem_category\n\n Biosample : ecosystem_subtype\n\n Biosample : ecosystem_type\n\n Biosample : efficiency_percent\n\n Biosample --|> QuantityValue : efficiency_percent\n\n Biosample : elev\n\n Biosample : elevator\n\n Biosample --|> TextValue : elevator\n\n Biosample : embargoed\n\n Biosample : emsl_biosample_identifiers\n\n Biosample : emulsions\n\n Biosample --|> TextValue : emulsions\n\n Biosample : env_broad_scale\n\n Biosample --|> ControlledIdentifiedTermValue : env_broad_scale\n\n Biosample : env_local_scale\n\n Biosample --|> ControlledIdentifiedTermValue : env_local_scale\n\n Biosample : env_medium\n\n Biosample --|> ControlledIdentifiedTermValue : env_medium\n\n Biosample : env_package\n\n Biosample --|> TextValue : env_package\n\n Biosample : environment_field\n\n Biosample : escalator\n\n Biosample --|> TextValue : escalator\n\n Biosample : ethylbenzene\n\n Biosample --|> QuantityValue : ethylbenzene\n\n Biosample : exp_duct\n\n Biosample --|> QuantityValue : exp_duct\n\n Biosample : exp_pipe\n\n Biosample --|> QuantityValue : exp_pipe\n\n Biosample : experimental_factor\n\n Biosample --|> ControlledTermValue : experimental_factor\n\n Biosample : experimental_factor_other\n\n Biosample : ext_door\n\n Biosample --|> TextValue : ext_door\n\n Biosample : ext_wall_orient\n\n Biosample --|> ext_wall_orient_enum : ext_wall_orient\n\n Biosample : ext_window_orient\n\n Biosample --|> ext_window_orient_enum : ext_window_orient\n\n Biosample : extreme_event\n\n Biosample : fao_class\n\n Biosample --|> fao_class_enum : fao_class\n\n Biosample : fertilizer_regm\n\n Biosample --|> TextValue : fertilizer_regm\n\n Biosample : field\n\n Biosample --|> TextValue : field\n\n Biosample : filter_method\n\n Biosample : filter_type\n\n Biosample --|> filter_type_enum : filter_type\n\n Biosample : fire\n\n Biosample : fireplace_type\n\n Biosample --|> TextValue : fireplace_type\n\n Biosample : flooding\n\n Biosample : floor_age\n\n Biosample --|> QuantityValue : floor_age\n\n Biosample : floor_area\n\n Biosample --|> QuantityValue : floor_area\n\n Biosample : floor_cond\n\n Biosample --|> floor_cond_enum : floor_cond\n\n Biosample : floor_count\n\n Biosample --|> TextValue : floor_count\n\n Biosample : floor_finish_mat\n\n Biosample --|> floor_finish_mat_enum : floor_finish_mat\n\n Biosample : floor_struc\n\n Biosample --|> floor_struc_enum : floor_struc\n\n Biosample : floor_thermal_mass\n\n Biosample --|> QuantityValue : floor_thermal_mass\n\n Biosample : floor_water_mold\n\n Biosample --|> floor_water_mold_enum : floor_water_mold\n\n Biosample : fluor\n\n Biosample --|> QuantityValue : fluor\n\n Biosample : freq_clean\n\n Biosample --|> QuantityValue : freq_clean\n\n Biosample : freq_cook\n\n Biosample --|> QuantityValue : freq_cook\n\n Biosample : fungicide_regm\n\n Biosample --|> TextValue : fungicide_regm\n\n Biosample : furniture\n\n Biosample --|> furniture_enum : furniture\n\n Biosample : gaseous_environment\n\n Biosample --|> TextValue : gaseous_environment\n\n Biosample : gaseous_substances\n\n Biosample --|> TextValue : gaseous_substances\n\n Biosample : gender_restroom\n\n Biosample --|> gender_restroom_enum : gender_restroom\n\n Biosample : genetic_mod\n\n Biosample --|> TextValue : genetic_mod\n\n Biosample : geo_loc_name\n\n Biosample --|> TextValue : geo_loc_name\n\n Biosample : glucosidase_act\n\n Biosample --|> QuantityValue : glucosidase_act\n\n Biosample : gold_biosample_identifiers\n\n Biosample : gravidity\n\n Biosample --|> TextValue : gravidity\n\n Biosample : gravity\n\n Biosample --|> TextValue : gravity\n\n Biosample : growth_facil\n\n Biosample --|> ControlledTermValue : growth_facil\n\n Biosample : growth_habit\n\n Biosample --|> growth_habit_enum : growth_habit\n\n Biosample : growth_hormone_regm\n\n Biosample --|> TextValue : growth_hormone_regm\n\n Biosample : habitat\n\n Biosample : hall_count\n\n Biosample --|> TextValue : hall_count\n\n Biosample : handidness\n\n Biosample --|> handidness_enum : handidness\n\n Biosample : has_numeric_value\n\n Biosample : has_raw_value\n\n Biosample : has_unit\n\n Biosample : hc_produced\n\n Biosample --|> hc_produced_enum : hc_produced\n\n Biosample : hcr\n\n Biosample --|> hcr_enum : hcr\n\n Biosample : hcr_fw_salinity\n\n Biosample --|> QuantityValue : hcr_fw_salinity\n\n Biosample : hcr_geol_age\n\n Biosample --|> hcr_geol_age_enum : hcr_geol_age\n\n Biosample : hcr_pressure\n\n Biosample --|> TextValue : hcr_pressure\n\n Biosample : hcr_temp\n\n Biosample --|> TextValue : hcr_temp\n\n Biosample : heat_cool_type\n\n Biosample --|> heat_cool_type_enum : heat_cool_type\n\n Biosample : heat_deliv_loc\n\n Biosample --|> heat_deliv_loc_enum : heat_deliv_loc\n\n Biosample : heat_sys_deliv_meth\n\n Biosample : heat_system_id\n\n Biosample --|> TextValue : heat_system_id\n\n Biosample : heavy_metals\n\n Biosample --|> TextValue : heavy_metals\n\n Biosample : heavy_metals_meth\n\n Biosample --|> TextValue : heavy_metals_meth\n\n Biosample : height_carper_fiber\n\n Biosample --|> QuantityValue : height_carper_fiber\n\n Biosample : herbicide_regm\n\n Biosample --|> TextValue : herbicide_regm\n\n Biosample : horizon_meth\n\n Biosample --|> TextValue : horizon_meth\n\n Biosample : host_age\n\n Biosample --|> QuantityValue : host_age\n\n Biosample : host_body_habitat\n\n Biosample --|> TextValue : host_body_habitat\n\n Biosample : host_body_product\n\n Biosample --|> ControlledTermValue : host_body_product\n\n Biosample : host_body_site\n\n Biosample --|> ControlledTermValue : host_body_site\n\n Biosample : host_body_temp\n\n Biosample --|> QuantityValue : host_body_temp\n\n Biosample : host_color\n\n Biosample --|> TextValue : host_color\n\n Biosample : host_common_name\n\n Biosample --|> TextValue : host_common_name\n\n Biosample : host_diet\n\n Biosample --|> TextValue : host_diet\n\n Biosample : host_dry_mass\n\n Biosample --|> QuantityValue : host_dry_mass\n\n Biosample : host_family_relation\n\n Biosample : host_genotype\n\n Biosample --|> TextValue : host_genotype\n\n Biosample : host_growth_cond\n\n Biosample --|> TextValue : host_growth_cond\n\n Biosample : host_height\n\n Biosample --|> QuantityValue : host_height\n\n Biosample : host_last_meal\n\n Biosample --|> TextValue : host_last_meal\n\n Biosample : host_length\n\n Biosample --|> QuantityValue : host_length\n\n Biosample : host_life_stage\n\n Biosample --|> TextValue : host_life_stage\n\n Biosample : host_name\n\n Biosample : host_phenotype\n\n Biosample --|> ControlledTermValue : host_phenotype\n\n Biosample : host_sex\n\n Biosample --|> host_sex_enum : host_sex\n\n Biosample : host_shape\n\n Biosample --|> TextValue : host_shape\n\n Biosample : host_subject_id\n\n Biosample --|> TextValue : host_subject_id\n\n Biosample : host_subspecf_genlin\n\n Biosample : host_substrate\n\n Biosample --|> TextValue : host_substrate\n\n Biosample : host_symbiont\n\n Biosample : host_taxid\n\n Biosample --|> ControlledIdentifiedTermValue : host_taxid\n\n Biosample : host_tot_mass\n\n Biosample --|> QuantityValue : host_tot_mass\n\n Biosample : host_wet_mass\n\n Biosample --|> QuantityValue : host_wet_mass\n\n Biosample : humidity\n\n Biosample --|> QuantityValue : humidity\n\n Biosample : humidity_regm\n\n Biosample --|> TextValue : humidity_regm\n\n Biosample : id\n\n Biosample : igsn_biosample_identifiers\n\n Biosample : img_identifiers\n\n Biosample : indoor_space\n\n Biosample --|> indoor_space_enum : indoor_space\n\n Biosample : indoor_surf\n\n Biosample --|> indoor_surf_enum : indoor_surf\n\n Biosample : indust_eff_percent\n\n Biosample --|> QuantityValue : indust_eff_percent\n\n Biosample : inorg_particles\n\n Biosample --|> TextValue : inorg_particles\n\n Biosample : insdc_biosample_identifiers\n\n Biosample : inside_lux\n\n Biosample --|> QuantityValue : inside_lux\n\n Biosample : int_wall_cond\n\n Biosample --|> int_wall_cond_enum : int_wall_cond\n\n Biosample : investigation_field\n\n Biosample : isotope_exposure\n\n Biosample : iw_bt_date_well\n\n Biosample --|> TimestampValue : iw_bt_date_well\n\n Biosample : iwf\n\n Biosample --|> QuantityValue : iwf\n\n Biosample : last_clean\n\n Biosample --|> TimestampValue : last_clean\n\n Biosample : lat_lon\n\n Biosample --|> GeolocationValue : lat_lon\n\n Biosample : lbc_thirty\n\n Biosample --|> QuantityValue : lbc_thirty\n\n Biosample : lbceq\n\n Biosample --|> QuantityValue : lbceq\n\n Biosample : light_intensity\n\n Biosample --|> QuantityValue : light_intensity\n\n Biosample : light_regm\n\n Biosample --|> TextValue : light_regm\n\n Biosample : light_type\n\n Biosample --|> light_type_enum : light_type\n\n Biosample : link_addit_analys\n\n Biosample --|> TextValue : link_addit_analys\n\n Biosample : link_class_info\n\n Biosample --|> TextValue : link_class_info\n\n Biosample : link_climate_info\n\n Biosample --|> TextValue : link_climate_info\n\n Biosample : lithology\n\n Biosample --|> lithology_enum : lithology\n\n Biosample : local_class\n\n Biosample --|> TextValue : local_class\n\n Biosample : local_class_meth\n\n Biosample --|> TextValue : local_class_meth\n\n Biosample : location\n\n Biosample : magnesium\n\n Biosample --|> QuantityValue : magnesium\n\n Biosample : manganese\n\n Biosample --|> QuantityValue : manganese\n\n Biosample : max_occup\n\n Biosample --|> QuantityValue : max_occup\n\n Biosample : mean_frict_vel\n\n Biosample --|> QuantityValue : mean_frict_vel\n\n Biosample : mean_peak_frict_vel\n\n Biosample --|> QuantityValue : mean_peak_frict_vel\n\n Biosample : mech_struc\n\n Biosample --|> mech_struc_enum : mech_struc\n\n Biosample : mechanical_damage\n\n Biosample --|> TextValue : mechanical_damage\n\n Biosample : methane\n\n Biosample --|> QuantityValue : methane\n\n Biosample : micro_biomass_c_meth\n\n Biosample : micro_biomass_meth\n\n Biosample : micro_biomass_n_meth\n\n Biosample : microbial_biomass\n\n Biosample --|> QuantityValue : microbial_biomass\n\n Biosample : microbial_biomass_c\n\n Biosample : microbial_biomass_n\n\n Biosample : mineral_nutr_regm\n\n Biosample --|> TextValue : mineral_nutr_regm\n\n Biosample : misc_param\n\n Biosample --|> TextValue : misc_param\n\n Biosample : mod_date\n\n Biosample : n_alkanes\n\n Biosample --|> TextValue : n_alkanes\n\n Biosample : name\n\n Biosample : ncbi_taxonomy_name\n\n Biosample : neon_biosample_identifiers\n\n Biosample : nitrate\n\n Biosample --|> QuantityValue : nitrate\n\n Biosample : nitrate_nitrogen\n\n Biosample --|> QuantityValue : nitrate_nitrogen\n\n Biosample : nitrite\n\n Biosample --|> QuantityValue : nitrite\n\n Biosample : nitrite_nitrogen\n\n Biosample --|> QuantityValue : nitrite_nitrogen\n\n Biosample : nitro\n\n Biosample --|> QuantityValue : nitro\n\n Biosample : non_microb_biomass\n\n Biosample : non_microb_biomass_method\n\n Biosample : non_min_nutr_regm\n\n Biosample : nucl_acid_amp\n\n Biosample --|> TextValue : nucl_acid_amp\n\n Biosample : nucl_acid_ext\n\n Biosample --|> TextValue : nucl_acid_ext\n\n Biosample : nucleic_acid_sequence_source_field\n\n Biosample : number_pets\n\n Biosample --|> QuantityValue : number_pets\n\n Biosample : number_plants\n\n Biosample --|> QuantityValue : number_plants\n\n Biosample : number_resident\n\n Biosample --|> QuantityValue : number_resident\n\n Biosample : occup_density_samp\n\n Biosample --|> QuantityValue : occup_density_samp\n\n Biosample : occup_document\n\n Biosample --|> occup_document_enum : occup_document\n\n Biosample : occup_samp\n\n Biosample --|> QuantityValue : occup_samp\n\n Biosample : org_carb\n\n Biosample --|> QuantityValue : org_carb\n\n Biosample : org_count_qpcr_info\n\n Biosample : org_matter\n\n Biosample --|> QuantityValue : org_matter\n\n Biosample : org_nitro\n\n Biosample --|> QuantityValue : org_nitro\n\n Biosample : org_nitro_method\n\n Biosample : org_particles\n\n Biosample --|> TextValue : org_particles\n\n Biosample : organism_count\n\n Biosample --|> QuantityValue : organism_count\n\n Biosample : other_treatment\n\n Biosample : owc_tvdss\n\n Biosample --|> QuantityValue : owc_tvdss\n\n Biosample : oxy_stat_samp\n\n Biosample --|> oxy_stat_samp_enum : oxy_stat_samp\n\n Biosample : oxygen\n\n Biosample --|> QuantityValue : oxygen\n\n Biosample : part_of\n\n Biosample --|> Study : part_of\n\n Biosample : part_org_carb\n\n Biosample --|> QuantityValue : part_org_carb\n\n Biosample : part_org_nitro\n\n Biosample --|> QuantityValue : part_org_nitro\n\n Biosample : particle_class\n\n Biosample --|> TextValue : particle_class\n\n Biosample : pcr_cond\n\n Biosample --|> TextValue : pcr_cond\n\n Biosample : pcr_primers\n\n Biosample --|> TextValue : pcr_primers\n\n Biosample : permeability\n\n Biosample --|> TextValue : permeability\n\n Biosample : perturbation\n\n Biosample --|> TextValue : perturbation\n\n Biosample : pesticide_regm\n\n Biosample --|> TextValue : pesticide_regm\n\n Biosample : petroleum_hydrocarb\n\n Biosample --|> QuantityValue : petroleum_hydrocarb\n\n Biosample : ph\n\n Biosample : ph_meth\n\n Biosample --|> TextValue : ph_meth\n\n Biosample : ph_regm\n\n Biosample --|> TextValue : ph_regm\n\n Biosample : phaeopigments\n\n Biosample --|> TextValue : phaeopigments\n\n Biosample : phosphate\n\n Biosample --|> QuantityValue : phosphate\n\n Biosample : phosplipid_fatt_acid\n\n Biosample --|> TextValue : phosplipid_fatt_acid\n\n Biosample : photon_flux\n\n Biosample --|> QuantityValue : photon_flux\n\n Biosample : plant_growth_med\n\n Biosample --|> ControlledTermValue : plant_growth_med\n\n Biosample : plant_product\n\n Biosample --|> TextValue : plant_product\n\n Biosample : plant_sex\n\n Biosample --|> plant_sex_enum : plant_sex\n\n Biosample : plant_struc\n\n Biosample --|> ControlledTermValue : plant_struc\n\n Biosample : pollutants\n\n Biosample --|> TextValue : pollutants\n\n Biosample : pool_dna_extracts\n\n Biosample --|> TextValue : pool_dna_extracts\n\n Biosample : porosity\n\n Biosample --|> TextValue : porosity\n\n Biosample : potassium\n\n Biosample --|> QuantityValue : potassium\n\n Biosample : pour_point\n\n Biosample --|> QuantityValue : pour_point\n\n Biosample : pre_treatment\n\n Biosample --|> TextValue : pre_treatment\n\n Biosample : pres_animal_insect\n\n Biosample : pressure\n\n Biosample --|> QuantityValue : pressure\n\n Biosample : prev_land_use_meth\n\n Biosample : previous_land_use\n\n Biosample --|> TextValue : previous_land_use\n\n Biosample : primary_prod\n\n Biosample --|> QuantityValue : primary_prod\n\n Biosample : primary_treatment\n\n Biosample --|> TextValue : primary_treatment\n\n Biosample : prod_rate\n\n Biosample --|> QuantityValue : prod_rate\n\n Biosample : prod_start_date\n\n Biosample --|> TimestampValue : prod_start_date\n\n Biosample : profile_position\n\n Biosample --|> profile_position_enum : profile_position\n\n Biosample : project_id\n\n Biosample : proport_woa_temperature\n\n Biosample : proposal_dna\n\n Biosample : proposal_rna\n\n Biosample : quad_pos\n\n Biosample --|> quad_pos_enum : quad_pos\n\n Biosample : radiation_regm\n\n Biosample --|> TextValue : radiation_regm\n\n Biosample : rainfall_regm\n\n Biosample --|> TextValue : rainfall_regm\n\n Biosample : reactor_type\n\n Biosample --|> TextValue : reactor_type\n\n Biosample : redox_potential\n\n Biosample --|> QuantityValue : redox_potential\n\n Biosample : rel_air_humidity\n\n Biosample --|> QuantityValue : rel_air_humidity\n\n Biosample : rel_humidity_out\n\n Biosample --|> QuantityValue : rel_humidity_out\n\n Biosample : rel_samp_loc\n\n Biosample --|> rel_samp_loc_enum : rel_samp_loc\n\n Biosample : replicate_number\n\n Biosample : reservoir\n\n Biosample --|> TextValue : reservoir\n\n Biosample : resins_pc\n\n Biosample --|> TextValue : resins_pc\n\n Biosample : rna_absorb1\n\n Biosample : rna_absorb2\n\n Biosample : rna_collect_site\n\n Biosample : rna_concentration\n\n Biosample : rna_cont_type\n\n Biosample --|> JgiContTypeEnum : rna_cont_type\n\n Biosample : rna_cont_well\n\n Biosample : rna_container_id\n\n Biosample : rna_isolate_meth\n\n Biosample : rna_organisms\n\n Biosample : rna_project_contact\n\n Biosample : rna_samp_id\n\n Biosample : rna_sample_format\n\n Biosample --|> rna_sample_format_enum : rna_sample_format\n\n Biosample : rna_sample_name\n\n Biosample : rna_seq_project\n\n Biosample : rna_seq_project_name\n\n Biosample : rna_seq_project_pi\n\n Biosample : rna_volume\n\n Biosample : room_air_exch_rate\n\n Biosample --|> QuantityValue : room_air_exch_rate\n\n Biosample : room_architec_elem\n\n Biosample : room_condt\n\n Biosample --|> room_condt_enum : room_condt\n\n Biosample : room_connected\n\n Biosample --|> room_connected_enum : room_connected\n\n Biosample : room_count\n\n Biosample --|> TextValue : room_count\n\n Biosample : room_dim\n\n Biosample --|> TextValue : room_dim\n\n Biosample : room_door_dist\n\n Biosample --|> TextValue : room_door_dist\n\n Biosample : room_door_share\n\n Biosample --|> TextValue : room_door_share\n\n Biosample : room_hallway\n\n Biosample --|> TextValue : room_hallway\n\n Biosample : room_loc\n\n Biosample --|> room_loc_enum : room_loc\n\n Biosample : room_moist_dam_hist\n\n Biosample : room_net_area\n\n Biosample --|> TextValue : room_net_area\n\n Biosample : room_occup\n\n Biosample --|> QuantityValue : room_occup\n\n Biosample : room_samp_pos\n\n Biosample --|> room_samp_pos_enum : room_samp_pos\n\n Biosample : room_type\n\n Biosample --|> room_type_enum : room_type\n\n Biosample : room_vol\n\n Biosample --|> TextValue : room_vol\n\n Biosample : room_wall_share\n\n Biosample --|> TextValue : room_wall_share\n\n Biosample : room_window_count\n\n Biosample : root_cond\n\n Biosample --|> TextValue : root_cond\n\n Biosample : root_med_carbon\n\n Biosample --|> TextValue : root_med_carbon\n\n Biosample : root_med_macronutr\n\n Biosample --|> TextValue : root_med_macronutr\n\n Biosample : root_med_micronutr\n\n Biosample --|> TextValue : root_med_micronutr\n\n Biosample : root_med_ph\n\n Biosample --|> QuantityValue : root_med_ph\n\n Biosample : root_med_regl\n\n Biosample --|> TextValue : root_med_regl\n\n Biosample : root_med_solid\n\n Biosample --|> TextValue : root_med_solid\n\n Biosample : root_med_suppl\n\n Biosample --|> TextValue : root_med_suppl\n\n Biosample : salinity\n\n Biosample --|> QuantityValue : salinity\n\n Biosample : salinity_category\n\n Biosample : salinity_meth\n\n Biosample --|> TextValue : salinity_meth\n\n Biosample : salt_regm\n\n Biosample --|> TextValue : salt_regm\n\n Biosample : samp_capt_status\n\n Biosample --|> samp_capt_status_enum : samp_capt_status\n\n Biosample : samp_collec_device\n\n Biosample : samp_collec_method\n\n Biosample : samp_collect_point\n\n Biosample --|> samp_collect_point_enum : samp_collect_point\n\n Biosample : samp_dis_stage\n\n Biosample --|> samp_dis_stage_enum : samp_dis_stage\n\n Biosample : samp_floor\n\n Biosample --|> samp_floor_enum : samp_floor\n\n Biosample : samp_loc_corr_rate\n\n Biosample --|> TextValue : samp_loc_corr_rate\n\n Biosample : samp_mat_process\n\n Biosample --|> ControlledTermValue : samp_mat_process\n\n Biosample : samp_md\n\n Biosample --|> QuantityValue : samp_md\n\n Biosample : samp_name\n\n Biosample : samp_preserv\n\n Biosample --|> TextValue : samp_preserv\n\n Biosample : samp_room_id\n\n Biosample --|> TextValue : samp_room_id\n\n Biosample : samp_size\n\n Biosample --|> QuantityValue : samp_size\n\n Biosample : samp_sort_meth\n\n Biosample --|> TextValue : samp_sort_meth\n\n Biosample : samp_store_dur\n\n Biosample --|> TextValue : samp_store_dur\n\n Biosample : samp_store_loc\n\n Biosample --|> TextValue : samp_store_loc\n\n Biosample : samp_store_temp\n\n Biosample --|> QuantityValue : samp_store_temp\n\n Biosample : samp_subtype\n\n Biosample --|> samp_subtype_enum : samp_subtype\n\n Biosample : samp_taxon_id\n\n Biosample --|> ControlledIdentifiedTermValue : samp_taxon_id\n\n Biosample : samp_time_out\n\n Biosample --|> TextValue : samp_time_out\n\n Biosample : samp_transport_cond\n\n Biosample --|> TextValue : samp_transport_cond\n\n Biosample : samp_tvdss\n\n Biosample --|> TextValue : samp_tvdss\n\n Biosample : samp_type\n\n Biosample --|> TextValue : samp_type\n\n Biosample : samp_vol_we_dna_ext\n\n Biosample --|> QuantityValue : samp_vol_we_dna_ext\n\n Biosample : samp_weather\n\n Biosample --|> samp_weather_enum : samp_weather\n\n Biosample : samp_well_name\n\n Biosample --|> TextValue : samp_well_name\n\n Biosample : sample_collection_site\n\n Biosample : sample_link\n\n Biosample : sample_shipped\n\n Biosample : sample_type\n\n Biosample --|> sample_type_enum : sample_type\n\n Biosample : saturates_pc\n\n Biosample --|> TextValue : saturates_pc\n\n Biosample : season\n\n Biosample --|> TextValue : season\n\n Biosample : season_environment\n\n Biosample --|> TextValue : season_environment\n\n Biosample : season_precpt\n\n Biosample --|> QuantityValue : season_precpt\n\n Biosample : season_temp\n\n Biosample --|> QuantityValue : season_temp\n\n Biosample : season_use\n\n Biosample --|> season_use_enum : season_use\n\n Biosample : secondary_treatment\n\n Biosample --|> TextValue : secondary_treatment\n\n Biosample : sediment_type\n\n Biosample --|> sediment_type_enum : sediment_type\n\n Biosample : seq_meth\n\n Biosample --|> TextValue : seq_meth\n\n Biosample : seq_quality_check\n\n Biosample --|> TextValue : seq_quality_check\n\n Biosample : sequencing_field\n\n Biosample : sewage_type\n\n Biosample --|> TextValue : sewage_type\n\n Biosample : shad_dev_water_mold\n\n Biosample : shading_device_cond\n\n Biosample --|> shading_device_cond_enum : shading_device_cond\n\n Biosample : shading_device_loc\n\n Biosample --|> TextValue : shading_device_loc\n\n Biosample : shading_device_mat\n\n Biosample --|> TextValue : shading_device_mat\n\n Biosample : shading_device_type\n\n Biosample --|> shading_device_type_enum : shading_device_type\n\n Biosample : sieving\n\n Biosample --|> TextValue : sieving\n\n Biosample : silicate\n\n Biosample --|> QuantityValue : silicate\n\n Biosample : size_frac\n\n Biosample --|> TextValue : size_frac\n\n Biosample : size_frac_low\n\n Biosample --|> QuantityValue : size_frac_low\n\n Biosample : size_frac_up\n\n Biosample --|> QuantityValue : size_frac_up\n\n Biosample : slope_aspect\n\n Biosample --|> QuantityValue : slope_aspect\n\n Biosample : slope_gradient\n\n Biosample --|> QuantityValue : slope_gradient\n\n Biosample : sludge_retent_time\n\n Biosample --|> QuantityValue : sludge_retent_time\n\n Biosample : sodium\n\n Biosample --|> QuantityValue : sodium\n\n Biosample : soil_horizon\n\n Biosample --|> soil_horizon_enum : soil_horizon\n\n Biosample : soil_text_measure\n\n Biosample --|> QuantityValue : soil_text_measure\n\n Biosample : soil_texture_meth\n\n Biosample : soil_type\n\n Biosample --|> TextValue : soil_type\n\n Biosample : soil_type_meth\n\n Biosample --|> TextValue : soil_type_meth\n\n Biosample : solar_irradiance\n\n Biosample --|> QuantityValue : solar_irradiance\n\n Biosample : soluble_inorg_mat\n\n Biosample --|> TextValue : soluble_inorg_mat\n\n Biosample : soluble_iron_micromol\n\n Biosample : soluble_org_mat\n\n Biosample --|> TextValue : soluble_org_mat\n\n Biosample : soluble_react_phosp\n\n Biosample --|> QuantityValue : soluble_react_phosp\n\n Biosample : source_mat_id\n\n Biosample --|> TextValue : source_mat_id\n\n Biosample : space_typ_state\n\n Biosample --|> TextValue : space_typ_state\n\n Biosample : specific\n\n Biosample --|> specific_enum : specific\n\n Biosample : specific_ecosystem\n\n Biosample : specific_humidity\n\n Biosample --|> QuantityValue : specific_humidity\n\n Biosample : sr_dep_env\n\n Biosample --|> sr_dep_env_enum : sr_dep_env\n\n Biosample : sr_geol_age\n\n Biosample --|> sr_geol_age_enum : sr_geol_age\n\n Biosample : sr_kerog_type\n\n Biosample --|> sr_kerog_type_enum : sr_kerog_type\n\n Biosample : sr_lithology\n\n Biosample --|> sr_lithology_enum : sr_lithology\n\n Biosample : standing_water_regm\n\n Biosample --|> TextValue : standing_water_regm\n\n Biosample : start_date_inc\n\n Biosample : start_time_inc\n\n Biosample : store_cond\n\n Biosample --|> TextValue : store_cond\n\n Biosample : substructure_type\n\n Biosample --|> substructure_type_enum : substructure_type\n\n Biosample : subsurface_depth\n\n Biosample --|> QuantityValue : subsurface_depth\n\n Biosample : sulfate\n\n Biosample --|> QuantityValue : sulfate\n\n Biosample : sulfate_fw\n\n Biosample --|> QuantityValue : sulfate_fw\n\n Biosample : sulfide\n\n Biosample --|> QuantityValue : sulfide\n\n Biosample : surf_air_cont\n\n Biosample --|> surf_air_cont_enum : surf_air_cont\n\n Biosample : surf_humidity\n\n Biosample --|> QuantityValue : surf_humidity\n\n Biosample : surf_material\n\n Biosample --|> surf_material_enum : surf_material\n\n Biosample : surf_moisture\n\n Biosample --|> QuantityValue : surf_moisture\n\n Biosample : surf_moisture_ph\n\n Biosample : surf_temp\n\n Biosample --|> QuantityValue : surf_temp\n\n Biosample : suspend_part_matter\n\n Biosample --|> QuantityValue : suspend_part_matter\n\n Biosample : suspend_solids\n\n Biosample --|> TextValue : suspend_solids\n\n Biosample : tan\n\n Biosample --|> QuantityValue : tan\n\n Biosample : target_gene\n\n Biosample --|> TextValue : target_gene\n\n Biosample : target_subfragment\n\n Biosample --|> TextValue : target_subfragment\n\n Biosample : technical_reps\n\n Biosample : temp\n\n Biosample --|> QuantityValue : temp\n\n Biosample : temp_out\n\n Biosample --|> QuantityValue : temp_out\n\n Biosample : tertiary_treatment\n\n Biosample --|> TextValue : tertiary_treatment\n\n Biosample : tidal_stage\n\n Biosample --|> tidal_stage_enum : tidal_stage\n\n Biosample : tillage\n\n Biosample --|> tillage_enum : tillage\n\n Biosample : tiss_cult_growth_med\n\n Biosample --|> TextValue : tiss_cult_growth_med\n\n Biosample : toluene\n\n Biosample --|> QuantityValue : toluene\n\n Biosample : tot_carb\n\n Biosample --|> QuantityValue : tot_carb\n\n Biosample : tot_depth_water_col\n\n Biosample --|> QuantityValue : tot_depth_water_col\n\n Biosample : tot_diss_nitro\n\n Biosample --|> QuantityValue : tot_diss_nitro\n\n Biosample : tot_inorg_nitro\n\n Biosample --|> QuantityValue : tot_inorg_nitro\n\n Biosample : tot_iron\n\n Biosample --|> QuantityValue : tot_iron\n\n Biosample : tot_nitro\n\n Biosample --|> QuantityValue : tot_nitro\n\n Biosample : tot_nitro_cont_meth\n\n Biosample : tot_nitro_content\n\n Biosample --|> QuantityValue : tot_nitro_content\n\n Biosample : tot_org_c_meth\n\n Biosample --|> TextValue : tot_org_c_meth\n\n Biosample : tot_org_carb\n\n Biosample --|> QuantityValue : tot_org_carb\n\n Biosample : tot_part_carb\n\n Biosample --|> QuantityValue : tot_part_carb\n\n Biosample : tot_phosp\n\n Biosample --|> QuantityValue : tot_phosp\n\n Biosample : tot_phosphate\n\n Biosample --|> QuantityValue : tot_phosphate\n\n Biosample : tot_sulfur\n\n Biosample --|> QuantityValue : tot_sulfur\n\n Biosample : train_line\n\n Biosample --|> train_line_enum : train_line\n\n Biosample : train_stat_loc\n\n Biosample --|> train_stat_loc_enum : train_stat_loc\n\n Biosample : train_stop_loc\n\n Biosample --|> train_stop_loc_enum : train_stop_loc\n\n Biosample : turbidity\n\n Biosample --|> QuantityValue : turbidity\n\n Biosample : tvdss_of_hcr_press\n\n Biosample --|> QuantityValue : tvdss_of_hcr_press\n\n Biosample : tvdss_of_hcr_temp\n\n Biosample --|> QuantityValue : tvdss_of_hcr_temp\n\n Biosample : typ_occup_density\n\n Biosample : type\n\n Biosample : ventilation_rate\n\n Biosample --|> QuantityValue : ventilation_rate\n\n Biosample : ventilation_type\n\n Biosample --|> TextValue : ventilation_type\n\n Biosample : vfa\n\n Biosample --|> QuantityValue : vfa\n\n Biosample : vfa_fw\n\n Biosample --|> QuantityValue : vfa_fw\n\n Biosample : vis_media\n\n Biosample --|> vis_media_enum : vis_media\n\n Biosample : viscosity\n\n Biosample --|> TextValue : viscosity\n\n Biosample : volatile_org_comp\n\n Biosample --|> TextValue : volatile_org_comp\n\n Biosample : wall_area\n\n Biosample --|> QuantityValue : wall_area\n\n Biosample : wall_const_type\n\n Biosample --|> wall_const_type_enum : wall_const_type\n\n Biosample : wall_finish_mat\n\n Biosample --|> wall_finish_mat_enum : wall_finish_mat\n\n Biosample : wall_height\n\n Biosample --|> QuantityValue : wall_height\n\n Biosample : wall_loc\n\n Biosample --|> wall_loc_enum : wall_loc\n\n Biosample : wall_surf_treatment\n\n Biosample --|> wall_surf_treatment_enum : wall_surf_treatment\n\n Biosample : wall_texture\n\n Biosample --|> wall_texture_enum : wall_texture\n\n Biosample : wall_thermal_mass\n\n Biosample --|> QuantityValue : wall_thermal_mass\n\n Biosample : wall_water_mold\n\n Biosample --|> TextValue : wall_water_mold\n\n Biosample : wastewater_type\n\n Biosample --|> TextValue : wastewater_type\n\n Biosample : water_cont_soil_meth\n\n Biosample : water_content\n\n Biosample : water_current\n\n Biosample --|> QuantityValue : water_current\n\n Biosample : water_cut\n\n Biosample --|> QuantityValue : water_cut\n\n Biosample : water_feat_size\n\n Biosample --|> QuantityValue : water_feat_size\n\n Biosample : water_feat_type\n\n Biosample --|> water_feat_type_enum : water_feat_type\n\n Biosample : water_prod_rate\n\n Biosample --|> QuantityValue : water_prod_rate\n\n Biosample : water_temp_regm\n\n Biosample --|> TextValue : water_temp_regm\n\n Biosample : watering_regm\n\n Biosample --|> TextValue : watering_regm\n\n Biosample : weekday\n\n Biosample --|> weekday_enum : weekday\n\n Biosample : win\n\n Biosample --|> TextValue : win\n\n Biosample : wind_direction\n\n Biosample --|> TextValue : wind_direction\n\n Biosample : wind_speed\n\n Biosample --|> QuantityValue : wind_speed\n\n Biosample : window_cond\n\n Biosample --|> window_cond_enum : window_cond\n\n Biosample : window_cover\n\n Biosample --|> window_cover_enum : window_cover\n\n Biosample : window_horiz_pos\n\n Biosample --|> window_horiz_pos_enum : window_horiz_pos\n\n Biosample : window_loc\n\n Biosample --|> window_loc_enum : window_loc\n\n Biosample : window_mat\n\n Biosample --|> window_mat_enum : window_mat\n\n Biosample : window_open_freq\n\n Biosample --|> TextValue : window_open_freq\n\n Biosample : window_size\n\n Biosample --|> TextValue : window_size\n\n Biosample : window_status\n\n Biosample --|> TextValue : window_status\n\n Biosample : window_type\n\n Biosample --|> window_type_enum : window_type\n\n Biosample : window_vert_pos\n\n Biosample --|> window_vert_pos_enum : window_vert_pos\n\n Biosample : window_water_mold\n\n Biosample --|> TextValue : window_water_mold\n\n Biosample : xylene\n\n Biosample --|> QuantityValue : xylene\n\n Biosample : zinc\n\n Biosample --|> QuantityValue : zinc\n\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\ntodos:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslots:\n- neon_biosample_identifiers\n- host_taxid\n- embargoed\n- collected_from\n- type\n- img_identifiers\n- samp_name\n- biosample_categories\n- type\n- part_of\n- id\n- alternative_identifiers\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chimera_check\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- has numeric value\n- has raw value\n- has unit\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucl_acid_amp\n- nucl_acid_ext\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- pcr_cond\n- pcr_primers\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- pool_dna_extracts\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_vol_we_dna_ext\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- seq_meth\n- seq_quality_check\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- target_gene\n- target_subfragment\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n oxy_stat_samp:\n name: oxy_stat_samp\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n domain_of:\n - Biosample\n range: uriorcurie\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n lat_lon:\n name: lat_lon\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n domain_of:\n - FieldResearchSite\n - Biosample\n env_broad_scale:\n name: env_broad_scale\n domain_of:\n - Biosample\n required: true\n env_local_scale:\n name: env_local_scale\n domain_of:\n - Biosample\n required: true\n env_medium:\n name: env_medium\n domain_of:\n - Biosample\n required: true\n part_of:\n name: part_of\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n domain_of:\n - Biosample\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n domain_of:\n - Biosample\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n domain_of:\n - Biosample\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n domain_of:\n - Biosample\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n domain_of:\n - Biosample\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n domain_of:\n - Biosample\n annual_precpt:\n name: annual_precpt\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n domain_of:\n - Biosample\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n domain_of:\n - FieldResearchSite\n - Biosample\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n domain_of:\n - Biosample\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n domain_of:\n - Biosample\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n domain_of:\n - Biosample\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n domain_of:\n - Biosample\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n domain_of:\n - Biosample\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n multivalued: true\n domain_of:\n - Biosample\n range: string\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n domain_of:\n - Biosample\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n domain_of:\n - Biosample\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n domain_of:\n - Biosample\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n domain_of:\n - Biosample\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n domain_of:\n - Biosample\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n domain_of:\n - Biosample\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n domain_of:\n - Biosample\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n domain_of:\n - Biosample\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n domain_of:\n - Biosample\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n domain_of:\n - Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\n notes:\n - 'id is already required to be unique because it is the identifier in Biosample''s\n parent class, NamedThing. Remember, notes like this could be exposed to end\n users. CJM suggested YAML # comment'\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\ntodos:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: MaterialEntity\nslot_usage:\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n oxy_stat_samp:\n name: oxy_stat_samp\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n domain_of:\n - Biosample\n range: uriorcurie\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n lat_lon:\n name: lat_lon\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n domain_of:\n - FieldResearchSite\n - Biosample\n env_broad_scale:\n name: env_broad_scale\n domain_of:\n - Biosample\n required: true\n env_local_scale:\n name: env_local_scale\n domain_of:\n - Biosample\n required: true\n env_medium:\n name: env_medium\n domain_of:\n - Biosample\n required: true\n part_of:\n name: part_of\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n domain_of:\n - Biosample\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n domain_of:\n - Biosample\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n domain_of:\n - Biosample\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n domain_of:\n - Biosample\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n domain_of:\n - Biosample\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n domain_of:\n - Biosample\n annual_precpt:\n name: annual_precpt\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n domain_of:\n - Biosample\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n domain_of:\n - FieldResearchSite\n - Biosample\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n domain_of:\n - Biosample\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n domain_of:\n - Biosample\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n domain_of:\n - Biosample\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n domain_of:\n - Biosample\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n domain_of:\n - Biosample\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n multivalued: true\n domain_of:\n - Biosample\n range: string\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n domain_of:\n - Biosample\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n domain_of:\n - Biosample\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n domain_of:\n - Biosample\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n domain_of:\n - Biosample\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n domain_of:\n - Biosample\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n domain_of:\n - Biosample\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n domain_of:\n - Biosample\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n domain_of:\n - Biosample\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n domain_of:\n - Biosample\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n domain_of:\n - Biosample\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n domain_of:\n - Biosample\nattributes:\n neon_biosample_identifiers:\n name: neon_biosample_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - neon_identifiers\n multivalued: true\n alias: neon_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n host_taxid:\n name: host_taxid\n annotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: NCBI taxon id of the host, e.g. 9606\n title: host taxid\n comments:\n - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host taxid\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000250\n multivalued: false\n alias: host_taxid\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n embargoed:\n name: embargoed\n description: If true, the data are embargoed and not available for public access.\n todos:\n - make this required?\n - first apply to Biosample\n - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n - applying to a Study may nto be granular enough\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: embargoed\n owner: Biosample\n domain_of:\n - Biosample\n range: boolean\n recommended: true\n collected_from:\n name: collected_from\n description: The Site from which a Biosample was collected\n todos:\n - add an OBO slot_uri ?\n comments:\n - this illustrates implementing a Biosample relation with a (binary) slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Biosample\n alias: collected_from\n owner: Biosample\n domain_of:\n - Biosample\n range: FieldResearchSite\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: Biosample\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n multivalued: true\n alias: img_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n samp_name:\n name: samp_name\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A local identifier or name that for the material sample used for\n extracting nucleic acids, and subsequent sequencing. It can refer either to\n the original material collected or to any derived sub-samples. It can have any\n format, but we suggest that you make it concise, unique and consistent within\n your lab, and as informative as possible. INSDC requires every sample name from\n a single Submitter to be unique. Use of a globally unique identifier for the\n field source_mat_id is recommended in addition to sample_name.\n title: sample name\n examples:\n - value: ISDsoil1\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample name\n rank: 1000\n is_a: investigation field\n string_serialization: '{text}'\n slot_uri: MIXS:0001107\n multivalued: false\n alias: samp_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n biosample_categories:\n name: biosample_categories\n title: Categories the biosample belongs to\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: biosample_categories\n owner: Biosample\n domain_of:\n - Biosample\n range: BiosampleCategoryEnum\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n required: true\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a biosample submitted to additional resources.\n Matches the entity that has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n multivalued: true\n alias: gold_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: uriorcurie\n pattern: ^gold:Gb[0-9]+$\n insdc_biosample_identifiers:\n name: insdc_biosample_identifiers\n description: identifiers for corresponding sample in INSDC\n examples:\n - value: https://bioregistry.io/biosample:SAMEA5989477\n - value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational\n gradients\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/bioregistry/bioregistry/issues/108\n - https://www.ebi.ac.uk/biosamples/\n - https://www.ncbi.nlm.nih.gov/biosample\n - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n aliases:\n - EBI biosample identifiers\n - NCBI biosample identifiers\n - DDBJ biosample identifiers\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - insdc_identifiers\n multivalued: true\n alias: insdc_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n emsl_biosample_identifiers:\n name: emsl_biosample_identifiers\n description: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\n title: EMSL Biosample Identifiers\n todos:\n - removed \"planned\" once NEXUS is online\n - determine real expansion for emsl prefix\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - emsl_identifiers\n multivalued: true\n alias: emsl_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n igsn_biosample_identifiers:\n name: igsn_biosample_identifiers\n description: A list of identifiers for the biosample from the IGSN database.\n title: IGSN Biosample Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - igsn_identifiers\n multivalued: true\n alias: igsn_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n abs_air_humidity:\n name: abs_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\n description: Actual mass of water vapor - mh20 - present in the air water vapor\n mixture\n title: absolute air humidity\n examples:\n - value: 9 gram per gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - absolute air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000122\n multivalued: false\n alias: abs_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_recov_method:\n name: add_recov_method\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one\n of them. If \"other\" is specified, please propose entry in \"additional info\"\n field\n title: secondary and tertiary recovery methods and start date\n examples:\n - value: Polymer Addition;2018-06-21T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary and tertiary recovery methods and start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001009\n multivalued: false\n alias: add_recov_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n additional_info:\n name: additional_info\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\n title: additional info\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - additional info\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000300\n multivalued: false\n alias: additional_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n address:\n name: address\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The street name and building number where the sampling occurred.\n title: address\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - address\n rank: 1000\n is_a: core field\n string_serialization: '{integer}{text}'\n slot_uri: MIXS:0000218\n multivalued: false\n alias: address\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n adj_room:\n name: adj_room\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms (room number, room name) immediately adjacent to the\n sampling room\n title: adjacent rooms\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - adjacent rooms\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000219\n multivalued: false\n alias: adj_room\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n aero_struc:\n name: aero_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\n title: aerospace structure\n examples:\n - value: plane\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aerospace structure\n rank: 1000\n is_a: core field\n string_serialization: '[plane|glider]'\n slot_uri: MIXS:0000773\n multivalued: false\n alias: aero_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n agrochem_addition:\n name: agrochem_addition\n annotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n title: history/agrochemical additions\n examples:\n - value: roundup;5 milligram per liter;2018-06-21\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/agrochemical additions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{timestamp}'\n slot_uri: MIXS:0000639\n multivalued: true\n alias: agrochem_addition\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n air_PM_concen:\n name: air_PM_concen\n annotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances that remain suspended in the air, and\n comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n report multiple PM's by entering numeric values preceded by name of PM\n title: air particulate matter concentration\n examples:\n - value: PM2.5;10 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air particulate matter concentration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000108\n multivalued: true\n alias: air_PM_concen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n air_temp:\n name: air_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the air at the time of sampling\n title: air temperature\n examples:\n - value: 20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000124\n multivalued: false\n alias: air_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n air_temp_regm:\n name: air_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include different temperature regimens\n title: air temperature regimen\n examples:\n - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000551\n multivalued: true\n alias: air_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000607\n multivalued: false\n alias: al_sat\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000324\n multivalued: false\n alias: al_sat_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n alkalinity:\n name: alkalinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Alkalinity, the ability of a solution to neutralize acids to the\n equivalence point of carbonate or bicarbonate\n title: alkalinity\n examples:\n - value: 50 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000421\n multivalued: false\n alias: alkalinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n alkalinity_method:\n name: alkalinity_method\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\n description: Method used for alkalinity measurement\n title: alkalinity method\n examples:\n - value: titration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000298\n multivalued: false\n alias: alkalinity_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n alkyl_diethers:\n name: alkyl_diethers\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of alkyl diethers\n title: alkyl diethers\n examples:\n - value: 0.005 mole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkyl diethers\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000490\n multivalued: false\n alias: alkyl_diethers\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n alt:\n name: alt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as\n atmospheric layers and clouds. It is used to measure the height of an object\n which is above the earth's surface. In this context, the altitude measurement\n is the vertical distance between the earth's surface above sea level and the\n sampled position in the air\n title: altitude\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - altitude\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000094\n multivalued: false\n alias: alt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n aminopept_act:\n name: aminopept_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of aminopeptidase activity\n title: aminopeptidase activity\n examples:\n - value: 0.269 mole per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aminopeptidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000172\n multivalued: false\n alias: aminopept_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ammonium:\n name: ammonium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium in the sample\n title: ammonium\n examples:\n - value: 1.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ammonium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000427\n multivalued: false\n alias: ammonium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ammonium_nitrogen:\n name: ammonium_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium nitrogen in the sample\n title: ammonium nitrogen\n examples:\n - value: 2.3 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - ammonium_nitrogen\n - NH4-N\n rank: 1000\n is_a: attribute\n alias: ammonium_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n amount_light:\n name: amount_light\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The unit of illuminance and luminous emittance, measuring luminous\n flux per unit area\n title: amount of light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount of light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000140\n multivalued: false\n alias: amount_light\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ances_data:\n name: ances_data\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about either pedigree or other ancestral information\n description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n (meaning [(A x B) x B] x B)\n title: ancestral data\n examples:\n - value: A/3*B\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ancestral data\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000247\n multivalued: false\n alias: ances_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n annual_precpt:\n name: annual_precpt\n description: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: mean annual precipitation\n todos:\n - This is no longer matching the listed IRI from GSC, added example. When NMDC\n has its own slots, map this to the MIxS slot\n examples:\n - value: 8.94 inch\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000644\n multivalued: false\n alias: annual_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n annual_temp:\n name: annual_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean annual temperature\n title: mean annual temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000642\n multivalued: false\n alias: annual_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n antibiotic_regm:\n name: antibiotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving antibiotic administration;\n should include the name of antibiotic, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n antibiotic regimens\n title: antibiotic regimen\n examples:\n - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - antibiotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000553\n multivalued: true\n alias: antibiotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n api:\n name: api\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\n description: 'API gravity is a measure of how heavy or light a petroleum liquid\n is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n 31.1\u00ac\u221e API)'\n title: API gravity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - API gravity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000157\n multivalued: false\n alias: api\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n arch_struc:\n name: arch_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: An architectural structure is a human-made, free-standing, immobile\n outdoor construction\n title: architectural structure\n examples:\n - value: shed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - architectural structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000774\n multivalued: false\n alias: arch_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: arch_struc_enum\n aromatics_pc:\n name: aromatics_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: aromatics wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aromatics wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000133\n multivalued: false\n alias: aromatics_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n asphaltenes_pc:\n name: asphaltenes_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: asphaltenes wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - asphaltenes wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000135\n multivalued: false\n alias: asphaltenes_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n atmospheric_data:\n name: atmospheric_data\n annotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Measurement of atmospheric data; can include multiple data\n title: atmospheric data\n examples:\n - value: wind speed;9 knots\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - atmospheric data\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0001097\n multivalued: true\n alias: atmospheric_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n avg_dew_point:\n name: avg_dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of dew point measures taken at the beginning of every\n hour over a 24 hour period on the sampling day\n title: average dew point\n examples:\n - value: 25.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000141\n multivalued: false\n alias: avg_dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n avg_occup:\n name: avg_occup\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Daily average occupancy of room. Indicate the number of person(s)\n daily occupying the sampling room.\n title: average daily occupancy\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average daily occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000775\n multivalued: false\n alias: avg_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n avg_temp:\n name: avg_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of temperatures taken at the beginning of every hour\n over a 24 hour period on the sampling day\n title: average temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000142\n multivalued: false\n alias: avg_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bac_prod:\n name: bac_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Bacterial production in the water column measured by isotope uptake\n title: bacterial production\n examples:\n - value: 5 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000683\n multivalued: false\n alias: bac_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bac_resp:\n name: bac_resp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial respiration in the water column\n title: bacterial respiration\n examples:\n - value: 300 micromole oxygen per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial respiration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000684\n multivalued: false\n alias: bac_resp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bacteria_carb_prod:\n name: bacteria_carb_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial carbon production\n title: bacterial carbon production\n examples:\n - value: 2.53 microgram per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial carbon production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000173\n multivalued: false\n alias: bacteria_carb_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n barometric_press:\n name: barometric_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\n description: Force per unit area exerted against a surface by the weight of air\n above that surface\n title: barometric pressure\n examples:\n - value: 5 millibar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - barometric pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000096\n multivalued: false\n alias: barometric_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n basin:\n name: basin\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the basin (e.g. Campos)\n title: basin name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - basin name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000290\n multivalued: false\n alias: basin\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n bathroom_count:\n name: bathroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bathrooms in the building\n title: bathroom count\n examples:\n - value: '1'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bathroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000776\n multivalued: false\n alias: bathroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n bedroom_count:\n name: bedroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bedrooms in the building\n title: bedroom count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bedroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000777\n multivalued: false\n alias: bedroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n benzene:\n name: benzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of benzene in the sample\n title: benzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - benzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000153\n multivalued: false\n alias: benzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n biochem_oxygen_dem:\n name: biochem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of dissolved oxygen needed by aerobic biological organisms\n in a body of water to break down organic material present in a given water sample\n at certain temperature over a specific time period\n title: biochemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biochemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000653\n multivalued: false\n alias: biochem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n biocide:\n name: biocide\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of biocides (commercial name of product and supplier) and date\n of administration\n title: biocide administration\n examples:\n - value: ALPHA 1427;Baker Hughes;2008-01-23\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001011\n multivalued: false\n alias: biocide\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biocide_admin_method:\n name: biocide_admin_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of biocide administration (dose, frequency, duration, time\n elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n days)\n title: biocide administration method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n slot_uri: MIXS:0000456\n multivalued: false\n alias: biocide_admin_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biol_stat:\n name: biol_stat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The level of genome modification.\n title: biological status\n examples:\n - value: natural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biological status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000858\n multivalued: false\n alias: biol_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: biol_stat_enum\n biomass:\n name: biomass\n annotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g. Microbial, total. Can include multiple measurements\n title: biomass\n examples:\n - value: total;20 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biomass\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000174\n multivalued: true\n alias: biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biotic_regm:\n name: biotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\n title: biotic regimen\n examples:\n - value: sample inoculated with Rhizobium spp. Culture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001038\n multivalued: false\n alias: biotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n biotic_relationship:\n name: biotic_relationship\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n description: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with\n species Y. The target organism is the subject of the relationship, and the other\n organism(s) is the object\n title: observed biotic relationship\n examples:\n - value: free living\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed biotic relationship\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000028\n multivalued: false\n alias: biotic_relationship\n owner: Biosample\n domain_of:\n - Biosample\n range: biotic_relationship_enum\n bishomohopanol:\n name: bishomohopanol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bishomohopanol\n title: bishomohopanol\n examples:\n - value: 14 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bishomohopanol\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000175\n multivalued: false\n alias: bishomohopanol\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n blood_press_diast:\n name: blood_press_diast\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting diastolic blood pressure, measured as mm mercury\n title: host blood pressure diastolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure diastolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000258\n multivalued: false\n alias: blood_press_diast\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n blood_press_syst:\n name: blood_press_syst\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting systolic blood pressure, measured as mm mercury\n title: host blood pressure systolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure systolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000259\n multivalued: false\n alias: blood_press_syst\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n bromide:\n name: bromide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bromide\n title: bromide\n examples:\n - value: 0.05 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bromide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000176\n multivalued: false\n alias: bromide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n build_docs:\n name: build_docs\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building design, construction and operation documents\n title: design, construction, and operation documents\n examples:\n - value: maintenance plans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - design, construction, and operation documents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000787\n multivalued: false\n alias: build_docs\n owner: Biosample\n domain_of:\n - Biosample\n range: build_docs_enum\n build_occup_type:\n name: build_occup_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The primary function for which a building or discrete part of a building\n is intended to be used\n title: building occupancy type\n examples:\n - value: market\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building occupancy type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000761\n multivalued: true\n alias: build_occup_type\n owner: Biosample\n domain_of:\n - Biosample\n range: build_occup_type_enum\n building_setting:\n name: building_setting\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A location (geography) where a building is set\n title: building setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building setting\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000768\n multivalued: false\n alias: building_setting\n owner: Biosample\n domain_of:\n - Biosample\n range: building_setting_enum\n built_struc_age:\n name: built_struc_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\n description: The age of the built structure since construction\n title: built structure age\n examples:\n - value: '15'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000145\n multivalued: false\n alias: built_struc_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n built_struc_set:\n name: built_struc_set\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The characterization of the location of the built structure as high\n or low human density\n title: built structure setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure setting\n rank: 1000\n is_a: core field\n string_serialization: '[urban|rural]'\n slot_uri: MIXS:0000778\n multivalued: false\n alias: built_struc_set\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n built_struc_type:\n name: built_struc_type\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\n title: built structure type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000721\n multivalued: false\n alias: built_struc_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n calcium:\n name: calcium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of calcium in the sample\n title: calcium\n examples:\n - value: 0.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - calcium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000432\n multivalued: false\n alias: calcium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_dioxide:\n name: carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon dioxide (gas) amount or concentration at the time of sampling\n title: carbon dioxide\n examples:\n - value: 410 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000097\n multivalued: false\n alias: carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_monoxide:\n name: carb_monoxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon monoxide (gas) amount or concentration at the time of sampling\n title: carbon monoxide\n examples:\n - value: 0.1 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon monoxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000098\n multivalued: false\n alias: carb_monoxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n carb_nitro_ratio:\n name: carb_nitro_ratio\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ratio of amount or concentrations of carbon to nitrogen\n title: carbon/nitrogen ratio\n examples:\n - value: '0.417361111'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon/nitrogen ratio\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000310\n multivalued: false\n alias: carb_nitro_ratio\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_area:\n name: ceil_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the ceiling space within the room\n title: ceiling area\n examples:\n - value: 25 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000148\n multivalued: false\n alias: ceil_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_cond:\n name: ceil_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: ceiling condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000779\n multivalued: false\n alias: ceil_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_cond_enum\n ceil_finish_mat:\n name: ceil_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a ceiling\n title: ceiling finish material\n examples:\n - value: stucco\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000780\n multivalued: false\n alias: ceil_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_finish_mat_enum\n ceil_struc:\n name: ceil_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The construction format of the ceiling\n title: ceiling structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling structure\n rank: 1000\n is_a: core field\n string_serialization: '[wood frame|concrete]'\n slot_uri: MIXS:0000782\n multivalued: false\n alias: ceil_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ceil_texture:\n name: ceil_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a ceiling surface\n title: ceiling texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000783\n multivalued: false\n alias: ceil_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_texture_enum\n ceil_thermal_mass:\n name: ceil_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the ceiling to provide inertia against temperature\n fluctuations. Generally this means concrete that is exposed. A metal deck that\n supports a concrete slab will act thermally as long as it is exposed to room\n air flow\n title: ceiling thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000143\n multivalued: false\n alias: ceil_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ceil_type:\n name: ceil_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of ceiling according to the ceiling's appearance or construction\n title: ceiling type\n examples:\n - value: coffered\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000784\n multivalued: false\n alias: ceil_type\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_type_enum\n ceil_water_mold:\n name: ceil_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the ceiling\n title: ceiling signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000781\n multivalued: false\n alias: ceil_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chem_administration:\n name: chem_administration\n annotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\n description: List of chemical compounds administered to the host or site where\n sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n include multiple compounds. For chemical entities of biological interest ontology\n (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n title: chemical administration\n examples:\n - value: agar [CHEBI:2509];2018-05-11T20:00Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical administration\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]};{timestamp}'\n slot_uri: MIXS:0000751\n multivalued: true\n alias: chem_administration\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n chem_mutagen:\n name: chem_mutagen\n annotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple mutagen regimens\n title: chemical mutagen\n examples:\n - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical mutagen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000555\n multivalued: true\n alias: chem_mutagen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chem_oxygen_dem:\n name: chem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and\n nitrite\n title: chemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000656\n multivalued: false\n alias: chem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n chem_treat_method:\n name: chem_treat_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of chemical administration(dose, frequency, duration, time\n elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n hr; 0 days)\n title: chemical treatment method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n slot_uri: MIXS:0000457\n multivalued: false\n alias: chem_treat_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n chem_treatment:\n name: chem_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the\n product and name of the supplier should be provided. The date of administration\n should also be included\n title: chemical treatment\n examples:\n - value: ACCENT 1125;DOW;2010-11-17\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001012\n multivalued: false\n alias: chem_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n chimera_check:\n name: chimera_check\n annotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\n description: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised\n of two or more phylogenetically distinct parent sequences.\n title: chimera check software\n examples:\n - value: uchime;v4.1;default parameters\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chimera check software\n rank: 1000\n is_a: sequencing field\n string_serialization: '{software};{version};{parameters}'\n slot_uri: MIXS:0000052\n multivalued: false\n alias: chimera_check\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n chloride:\n name: chloride\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chloride in the sample\n title: chloride\n examples:\n - value: 5000 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chloride\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000429\n multivalued: false\n alias: chloride\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n chlorophyll:\n name: chlorophyll\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chlorophyll\n title: chlorophyll\n examples:\n - value: 5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chlorophyll\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000177\n multivalued: false\n alias: chlorophyll\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n climate_environment:\n name: climate_environment\n description: Treatment involving an exposure to a particular climate; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n climates\n title: climate environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001040\n multivalued: true\n alias: climate_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n collection_date:\n name: collection_date\n annotations:\n expected_value:\n tag: expected_value\n value: date and time\n description: 'The time of sampling, either as an instance (single point in time)\n or interval. In case no exact time is available, the date/time can be right\n truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n title: collection date\n examples:\n - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - collection date\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000011\n multivalued: false\n alias: collection_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n conduc:\n name: conduc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Electrical conductivity of water\n title: conductivity\n examples:\n - value: 10 milliSiemens per centimeter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - conductivity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000692\n multivalued: false\n alias: conduc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n cool_syst_id:\n name: cool_syst_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The cooling system identifier\n title: cooling system identifier\n examples:\n - value: '12345'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - cooling system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000785\n multivalued: false\n alias: cool_syst_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n core field:\n name: core field\n description: basic fields\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: core_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n crop_rotation:\n name: crop_rotation\n annotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not crop is rotated, and if yes, rotation schedule\n title: history/crop rotation\n examples:\n - value: yes;R2/2017-01-01/2018-12-31/P6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/crop rotation\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000318\n multivalued: false\n alias: crop_rotation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n cult_root_med:\n name: cult_root_med\n annotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Name or reference for the hydroponic or in vitro culture rooting\n medium; can be the name of a commonly used medium or reference to a specific\n medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n published, use the rooting medium descriptors.\n title: culture rooting medium\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - culture rooting medium\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001041\n multivalued: false\n alias: cult_root_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n cur_land_use:\n name: cur_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Present state of sample site\n title: current land use\n examples:\n - value: conifers\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current land use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001080\n multivalued: false\n alias: cur_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: cur_land_use_enum\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n multivalued: false\n alias: cur_vegetation\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n cur_vegetation_meth:\n name: cur_vegetation_meth\n description: Reference or method used in vegetation classification\n title: current vegetation method\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000314\n multivalued: false\n alias: cur_vegetation_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n date_last_rain:\n name: date_last_rain\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The date of the last time it rained\n title: date last rain\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - date last rain\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000786\n multivalued: false\n alias: date_last_rain\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n density:\n name: density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\n title: density\n examples:\n - value: 1000 kilogram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000435\n multivalued: false\n alias: density\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n depos_env:\n name: depos_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: depositional environment\n examples:\n - value: Continental - Alluvial\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000992\n multivalued: false\n alias: depos_env\n owner: Biosample\n domain_of:\n - Biosample\n range: depos_env_enum\n depth:\n name: depth\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth\n can be reported as an interval for subsurface samples.\n title: depth\n examples:\n - value: 10 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000018\n multivalued: false\n alias: depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dew_point:\n name: dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\n title: dew point\n examples:\n - value: 22 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000129\n multivalued: false\n alias: dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diether_lipids:\n name: diether_lipids\n annotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of diether lipids; can include multiple types of diether\n lipids\n title: diether lipids\n examples:\n - value: 0.2 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - diether lipids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000178\n multivalued: true\n alias: diether_lipids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n diss_carb_dioxide:\n name: diss_carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved carbon dioxide in the sample or liquid\n portion of the sample\n title: dissolved carbon dioxide\n examples:\n - value: 5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000436\n multivalued: false\n alias: diss_carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_hydrogen:\n name: diss_hydrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved hydrogen\n title: dissolved hydrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved hydrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000179\n multivalued: false\n alias: diss_hydrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_carb:\n name: diss_inorg_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved inorganic carbon concentration in the sample, typically\n measured after filtering the sample using a 0.45 micrometer filter\n title: dissolved inorganic carbon\n examples:\n - value: 2059 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000434\n multivalued: false\n alias: diss_inorg_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_nitro:\n name: diss_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic nitrogen\n title: dissolved inorganic nitrogen\n examples:\n - value: 761 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000698\n multivalued: false\n alias: diss_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_inorg_phosp:\n name: diss_inorg_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic phosphorus in the sample\n title: dissolved inorganic phosphorus\n examples:\n - value: 56.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000106\n multivalued: false\n alias: diss_inorg_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_iron:\n name: diss_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved iron in the sample\n title: dissolved iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000139\n multivalued: false\n alias: diss_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_org_carb:\n name: diss_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\n title: dissolved organic carbon\n examples:\n - value: 197 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000433\n multivalued: false\n alias: diss_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_org_nitro:\n name: diss_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\n title: dissolved organic nitrogen\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000162\n multivalued: false\n alias: diss_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_oxygen:\n name: diss_oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen\n title: dissolved oxygen\n examples:\n - value: 175 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000119\n multivalued: false\n alias: diss_oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n diss_oxygen_fluid:\n name: diss_oxygen_fluid\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen in the oil field produced fluids\n as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n title: dissolved oxygen in fluids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen in fluids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000438\n multivalued: false\n alias: diss_oxygen_fluid\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_cont_well:\n name: dna_cont_well\n title: DNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: dna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n door_comp_type:\n name: door_comp_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The composite type of the door\n title: door type, composite\n examples:\n - value: revolving\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, composite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000795\n multivalued: false\n alias: door_comp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_comp_type_enum\n door_cond:\n name: door_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The phsical condition of the door\n title: door condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000788\n multivalued: false\n alias: door_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: door_cond_enum\n door_direct:\n name: door_direct\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction the door opens\n title: door direction of opening\n examples:\n - value: inward\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door direction of opening\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000789\n multivalued: false\n alias: door_direct\n owner: Biosample\n domain_of:\n - Biosample\n range: door_direct_enum\n door_loc:\n name: door_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the door in the room\n title: door location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000790\n multivalued: false\n alias: door_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: door_loc_enum\n door_mat:\n name: door_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the door is composed of\n title: door material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000791\n multivalued: false\n alias: door_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: door_mat_enum\n door_move:\n name: door_move\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of movement of the door\n title: door movement\n examples:\n - value: swinging\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door movement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000792\n multivalued: false\n alias: door_move\n owner: Biosample\n domain_of:\n - Biosample\n range: door_move_enum\n door_size:\n name: door_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the door\n title: door area or size\n examples:\n - value: 2.5 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door area or size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000158\n multivalued: false\n alias: door_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n door_type:\n name: door_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of door material\n title: door type\n examples:\n - value: wooden\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000794\n multivalued: false\n alias: door_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_enum\n door_type_metal:\n name: door_type_metal\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of metal door\n title: door type, metal\n examples:\n - value: hollow\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, metal\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000796\n multivalued: false\n alias: door_type_metal\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_metal_enum\n door_type_wood:\n name: door_type_wood\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of wood door\n title: door type, wood\n examples:\n - value: battened\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, wood\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000797\n multivalued: false\n alias: door_type_wood\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_wood_enum\n door_water_mold:\n name: door_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a door\n title: door signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000793\n multivalued: false\n alias: door_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n down_par:\n name: down_par\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square\n centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Visible waveband radiance and irradiance measurements in the water\n column\n title: downward PAR\n examples:\n - value: 28.71 microEinstein per square meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - downward PAR\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000703\n multivalued: false\n alias: down_par\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n drainage_class:\n name: drainage_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Drainage classification from a standard system such as the USDA system\n title: drainage classification\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drainage classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001085\n multivalued: false\n alias: drainage_class\n owner: Biosample\n domain_of:\n - Biosample\n range: drainage_class_enum\n drawings:\n name: drawings\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The buildings architectural drawings; if design is chosen, indicate\n phase-conceptual, schematic, design development, and construction documents\n title: drawings\n examples:\n - value: sketch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drawings\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000798\n multivalued: false\n alias: drawings\n owner: Biosample\n domain_of:\n - Biosample\n range: drawings_enum\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n efficiency_percent:\n name: efficiency_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of volatile solids removed from the anaerobic digestor\n title: efficiency percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - efficiency percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000657\n multivalued: false\n alias: efficiency_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n elev:\n name: elev\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n multivalued: false\n alias: elev\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n elevator:\n name: elevator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of elevators within the built structure\n title: elevator count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000799\n multivalued: false\n alias: elevator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n emulsions:\n name: emulsions\n annotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as paints, adhesives,\n mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n types\n title: emulsions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - emulsions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000660\n multivalued: true\n alias: emulsions\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n env_broad_scale:\n name: env_broad_scale\n description: 'Report the major environmental system the sample or specimen came\n from. The system(s) identified should have a coarse spatial grain, to provide\n the general environmental context of where the sampling was done (e.g. in the\n desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n title: broad-scale environmental context\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000012\n multivalued: false\n alias: env_broad_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_local_scale:\n name: env_local_scale\n description: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial\n grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n title: local environmental context\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000013\n multivalued: false\n alias: env_local_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_medium:\n name: env_medium\n description: 'Report the environmental material(s) immediately surrounding the\n sample or specimen at the time of sampling. We recommend using subclasses of\n ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference\n mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n (e.g. a tree, a leaf, a table top).'\n title: environmental medium\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000014\n multivalued: false\n alias: env_medium\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n env_package:\n name: env_package\n description: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the\n name of the environmental package, a selection of fields can be made from the\n subtables and can be reported\n in_subset:\n - mixs extension\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental package\n rank: 1000\n is_a: attribute\n alias: env_package\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n environment field:\n name: environment field\n description: field describing environmental aspect of a sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: environment_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n escalator:\n name: escalator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of escalators within the built structure\n title: escalator count\n examples:\n - value: '4'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - escalator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000800\n multivalued: false\n alias: escalator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ethylbenzene:\n name: ethylbenzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ethylbenzene in the sample\n title: ethylbenzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ethylbenzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000155\n multivalued: false\n alias: ethylbenzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n exp_duct:\n name: exp_duct\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of exposed ductwork in the room\n title: exposed ductwork\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed ductwork\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000144\n multivalued: false\n alias: exp_duct\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n exp_pipe:\n name: exp_pipe\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exposed pipes in the room\n title: exposed pipes\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed pipes\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000220\n multivalued: false\n alias: exp_pipe\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n experimental_factor:\n name: experimental_factor\n annotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\n description: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in\n an increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n title: experimental factor\n examples:\n - value: time series design [EFO:EFO_0001779]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - experimental factor\n rank: 1000\n is_a: investigation field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000008\n multivalued: false\n alias: experimental_factor\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n ext_door:\n name: ext_door\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exterior doors in the built structure\n title: exterior door count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exterior door count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000170\n multivalued: false\n alias: ext_door\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ext_wall_orient:\n name: ext_wall_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The orientation of the exterior wall\n title: orientations of exterior wall\n examples:\n - value: northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior wall\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000817\n multivalued: false\n alias: ext_wall_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_wall_orient_enum\n ext_window_orient:\n name: ext_window_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The compass direction the exterior window of the room is facing\n title: orientations of exterior window\n examples:\n - value: southwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior window\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000818\n multivalued: false\n alias: ext_window_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_window_orient_enum\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n description: Unusual physical events that may have affected microbial populations\n title: history/extreme events\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n examples:\n - value: 1980-05-18, volcanic eruption\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000320\n multivalued: false\n alias: extreme_event\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n fao_class:\n name: fao_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification from the FAO World Reference Database for Soil\n Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n title: soil_taxonomic/FAO classification\n examples:\n - value: Luvisols\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/FAO classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001083\n multivalued: false\n alias: fao_class\n owner: Biosample\n domain_of:\n - Biosample\n range: fao_class_enum\n fertilizer_regm:\n name: fertilizer_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple fertilizer\n regimens\n title: fertilizer regimen\n examples:\n - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fertilizer regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000556\n multivalued: true\n alias: fertilizer_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n field:\n name: field\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the hydrocarbon field (e.g. Albacora)\n title: field name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - field name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000291\n multivalued: false\n alias: field\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n filter_type:\n name: filter_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: A device which removes solid particulates or airborne molecular contaminants\n title: filter type\n examples:\n - value: HEPA\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - filter type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000765\n multivalued: true\n alias: filter_type\n owner: Biosample\n domain_of:\n - Biosample\n range: filter_type_enum\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of fire\n title: history/fire\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001086\n multivalued: false\n alias: fire\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n fireplace_type:\n name: fireplace_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A firebox with chimney\n title: fireplace type\n examples:\n - value: wood burning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fireplace type\n rank: 1000\n is_a: core field\n string_serialization: '[gas burning|wood burning]'\n slot_uri: MIXS:0000802\n multivalued: false\n alias: fireplace_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of flooding\n title: history/flooding\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000319\n multivalued: false\n alias: flooding\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n floor_age:\n name: floor_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\n description: The time period since installment of the carpet or flooring\n title: floor age\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000164\n multivalued: false\n alias: floor_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_area:\n name: floor_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the floor space within the room\n title: floor area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000165\n multivalued: false\n alias: floor_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_cond:\n name: floor_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the floor at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: floor condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000803\n multivalued: false\n alias: floor_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_cond_enum\n floor_count:\n name: floor_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of floors in the building, including basements and mechanical\n penthouse\n title: floor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000225\n multivalued: false\n alias: floor_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n floor_finish_mat:\n name: floor_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor covering type; the finished surface that is walked on\n title: floor finish material\n examples:\n - value: carpet\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000804\n multivalued: false\n alias: floor_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_finish_mat_enum\n floor_struc:\n name: floor_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\n title: floor structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000806\n multivalued: false\n alias: floor_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_struc_enum\n floor_thermal_mass:\n name: floor_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the floor to provide inertia against temperature fluctuations\n title: floor thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000166\n multivalued: false\n alias: floor_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n floor_water_mold:\n name: floor_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew in a room\n title: floor signs of water/mold\n examples:\n - value: ceiling discoloration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor signs of water/mold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000805\n multivalued: false\n alias: floor_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_water_mold_enum\n fluor:\n name: fluor\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\n description: Raw or converted fluorescence of water\n title: fluorescence\n examples:\n - value: 2.5 volts\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fluorescence\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000704\n multivalued: false\n alias: fluor\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n freq_clean:\n name: freq_clean\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times the sample location is cleaned. Frequency of\n cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n title: frequency of cleaning\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cleaning\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000226\n multivalued: false\n alias: freq_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n freq_cook:\n name: freq_cook\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times a meal is cooked per week\n title: frequency of cooking\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cooking\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000227\n multivalued: false\n alias: freq_cook\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n fungicide_regm:\n name: fungicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fungicide regimens\n title: fungicide regimen\n examples:\n - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fungicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000557\n multivalued: true\n alias: fungicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n furniture:\n name: furniture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The types of furniture present in the sampled room\n title: furniture\n examples:\n - value: chair\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - furniture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000807\n multivalued: false\n alias: furniture\n owner: Biosample\n domain_of:\n - Biosample\n range: furniture_enum\n gaseous_environment:\n name: gaseous_environment\n description: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\n title: gaseous environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000558\n multivalued: true\n alias: gaseous_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gaseous_substances:\n name: gaseous_substances\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\n title: gaseous substances\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous substances\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000661\n multivalued: true\n alias: gaseous_substances\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gender_restroom:\n name: gender_restroom\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The gender type of the restroom\n title: gender of restroom\n examples:\n - value: male\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gender of restroom\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000808\n multivalued: false\n alias: gender_restroom\n owner: Biosample\n domain_of:\n - Biosample\n range: gender_restroom_enum\n genetic_mod:\n name: genetic_mod\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Genetic modifications of the genome of an organism, which may occur\n naturally by spontaneous mutation, or be introduced by some experimental means,\n e.g. specification of a transgene or the gene knocked-out or details of transient\n transfection\n title: genetic modification\n examples:\n - value: aox1A transgenic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - genetic modification\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000859\n multivalued: false\n alias: genetic_mod\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n multivalued: false\n alias: geo_loc_name\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n glucosidase_act:\n name: glucosidase_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of glucosidase activity\n title: glucosidase activity\n examples:\n - value: 5 mol per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - glucosidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000137\n multivalued: false\n alias: glucosidase_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n gravidity:\n name: gravidity\n annotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\n title: gravidity\n examples:\n - value: yes;due date:2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravidity\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{timestamp}'\n slot_uri: MIXS:0000875\n multivalued: false\n alias: gravidity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n gravity:\n name: gravity\n annotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity;\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple treatments\n title: gravity\n examples:\n - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000559\n multivalued: true\n alias: gravity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n growth_facil:\n name: growth_facil\n annotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n title: growth facility\n examples:\n - value: Growth chamber [CO_715:0000189]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth facility\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{termLabel} {[termID]}'\n slot_uri: MIXS:0001043\n multivalued: false\n alias: growth_facil\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n growth_habit:\n name: growth_habit\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Characteristic shape, appearance or growth form of a plant species\n title: growth habit\n examples:\n - value: spreading\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth habit\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001044\n multivalued: false\n alias: growth_habit\n owner: Biosample\n domain_of:\n - Biosample\n range: growth_habit_enum\n growth_hormone_regm:\n name: growth_hormone_regm\n annotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple growth\n hormone regimens\n title: growth hormone regimen\n examples:\n - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth hormone regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000560\n multivalued: true\n alias: growth_hormone_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n hall_count:\n name: hall_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of hallways and cooridors in the built structure\n title: hallway/corridor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hallway/corridor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000228\n multivalued: false\n alias: hall_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n handidness:\n name: handidness\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The handidness of the individual sampled\n title: handidness\n examples:\n - value: right handedness\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - handidness\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000809\n multivalued: false\n alias: handidness\n owner: Biosample\n domain_of:\n - Biosample\n range: handidness_enum\n has numeric value:\n name: has numeric value\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_numeric_value\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n has raw value:\n name: has raw value\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n string_serialization: '{has numeric value} {has unit}'\n alias: has_raw_value\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n has unit:\n name: has unit\n description: Example \"m\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_unit\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n hc_produced:\n name: hc_produced\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\n title: hydrocarbon type produced\n examples:\n - value: Gas\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon type produced\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000989\n multivalued: false\n alias: hc_produced\n owner: Biosample\n domain_of:\n - Biosample\n range: hc_produced_enum\n hcr:\n name: hcr\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n defined as a natural environmental feature containing large amounts of hydrocarbons\n at high concentrations potentially suitable for commercial exploitation. This\n term should not be confused with the Hydrocarbon Occurrence term which also\n includes hydrocarbon-rich environments with currently limited commercial interest\n such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n entry in \"additional info\" field\n title: hydrocarbon resource type\n examples:\n - value: Oil Sand\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000988\n multivalued: false\n alias: hcr\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_enum\n hcr_fw_salinity:\n name: hcr_fw_salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original formation water salinity (prior to secondary recovery e.g.\n Waterflooding) expressed as TDS\n title: formation water salinity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - formation water salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000406\n multivalued: false\n alias: hcr_fw_salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n hcr_geol_age:\n name: hcr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: hydrocarbon resource geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000993\n multivalued: false\n alias: hcr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_geol_age_enum\n hcr_pressure:\n name: hcr_pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\n description: Original pressure of the hydrocarbon resource\n title: hydrocarbon resource original pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original pressure\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000395\n multivalued: false\n alias: hcr_pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n hcr_temp:\n name: hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Original temperature of the hydrocarbon resource\n title: hydrocarbon resource original temperature\n examples:\n - value: 150-295 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original temperature\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000393\n multivalued: false\n alias: hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heat_cool_type:\n name: heat_cool_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Methods of conditioning or heating a room or building\n title: heating and cooling system type\n examples:\n - value: heat pump\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating and cooling system type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000766\n multivalued: true\n alias: heat_cool_type\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_cool_type_enum\n heat_deliv_loc:\n name: heat_deliv_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of heat delivery within the room\n title: heating delivery locations\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating delivery locations\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000810\n multivalued: false\n alias: heat_deliv_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_deliv_loc_enum\n heat_sys_deliv_meth:\n name: heat_sys_deliv_meth\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The method by which the heat is delivered through the system\n title: heating system delivery method\n examples:\n - value: radiant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system delivery method\n rank: 1000\n is_a: core field\n string_serialization: '[conductive|radiant]'\n slot_uri: MIXS:0000812\n multivalued: false\n alias: heat_sys_deliv_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n heat_system_id:\n name: heat_system_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The heating system identifier\n title: heating system identifier\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000833\n multivalued: false\n alias: heat_system_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Changed to multi-valued. In MIxS, you add another column to denote multiple\n heavy metals. We don't have that ability in the submission portal.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000652\n multivalued: true\n alias: heavy_metals\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n heavy_metals_meth:\n name: heavy_metals_meth\n description: Reference or method used in determining heavy metals\n title: heavy metals method/ extreme unusual properties\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000343\n multivalued: true\n alias: heavy_metals_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n height_carper_fiber:\n name: height_carper_fiber\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average carpet fiber height in the indoor environment\n title: height carpet fiber mat\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - height carpet fiber mat\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000167\n multivalued: false\n alias: height_carper_fiber\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n herbicide_regm:\n name: herbicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of\n herbicide, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple regimens\n title: herbicide regimen\n examples:\n - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - herbicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000561\n multivalued: true\n alias: herbicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n horizon_meth:\n name: horizon_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the horizon\n title: soil horizon method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000321\n multivalued: false\n alias: horizon_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_age:\n name: host_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\n title: host age\n examples:\n - value: 10 days\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000255\n multivalued: false\n alias: host_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_body_habitat:\n name: host_body_habitat\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Original body habitat where the sample was obtained from\n title: host body habitat\n examples:\n - value: nasopharynx\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body habitat\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000866\n multivalued: false\n alias: host_body_habitat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_body_product:\n name: host_body_product\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the body, e.g. Stool, mucus, where the sample\n was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n or https://www.ebi.ac.uk/ols/ontologies/uberon\n title: host body product\n examples:\n - value: Portion of mucus [fma66938]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body product\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000888\n multivalued: false\n alias: host_body_product\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_body_site:\n name: host_body_site\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n title: host body site\n examples:\n - value: gill [UBERON:0002535]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body site\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000867\n multivalued: false\n alias: host_body_site\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_body_temp:\n name: host_body_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Core body temperature of the host when sample was collected\n title: host body temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000274\n multivalued: false\n alias: host_body_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_color:\n name: host_color\n annotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\n description: The color of host\n title: host color\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host color\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000260\n multivalued: false\n alias: host_color\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_common_name:\n name: host_common_name\n annotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\n description: Common name of the host.\n title: host common name\n examples:\n - value: human\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host common name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000248\n multivalued: false\n alias: host_common_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_diet:\n name: host_diet\n annotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\n description: Type of diet depending on the host, for animals omnivore, herbivore\n etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n title: host diet\n examples:\n - value: herbivore\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host diet\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000869\n multivalued: true\n alias: host_diet\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_dry_mass:\n name: host_dry_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of dry mass\n title: host dry mass\n examples:\n - value: 500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host dry mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000257\n multivalued: false\n alias: host_dry_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_family_relation:\n name: host_family_relation\n annotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\n description: Familial relationships to other hosts in the same study; can include\n multiple relationships\n title: host family relationship\n examples:\n - value: offspring;Mussel25\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host family relationship\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0000872\n multivalued: true\n alias: host_family_relation\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_genotype:\n name: host_genotype\n annotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\n description: Observed genotype\n title: host genotype\n examples:\n - value: C57BL/6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host genotype\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000365\n multivalued: false\n alias: host_genotype\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_growth_cond:\n name: host_growth_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Literature reference giving growth conditions of the host\n title: host growth conditions\n examples:\n - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host growth conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000871\n multivalued: false\n alias: host_growth_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_height:\n name: host_height\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The height of subject\n title: host height\n examples:\n - value: 0.1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000264\n multivalued: false\n alias: host_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_last_meal:\n name: host_last_meal\n annotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\n description: Content of last meal and time since feeding; can include multiple\n values\n title: host last meal\n examples:\n - value: corn feed;P2H\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host last meal\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000870\n multivalued: true\n alias: host_last_meal\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_length:\n name: host_length\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length of subject\n title: host length\n examples:\n - value: 1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host length\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000256\n multivalued: false\n alias: host_length\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_life_stage:\n name: host_life_stage\n annotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of life stage of host\n title: host life stage\n examples:\n - value: adult\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host life stage\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000251\n multivalued: false\n alias: host_life_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_phenotype:\n name: host_phenotype\n annotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\n description: Phenotype of human or other host. For phenotypic quality ontology\n (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n title: host phenotype\n examples:\n - value: elongated [PATO:0001154]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host phenotype\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000874\n multivalued: false\n alias: host_phenotype\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n host_sex:\n name: host_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Gender or physical sex of the host.\n title: host sex\n examples:\n - value: non-binary\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000811\n multivalued: false\n alias: host_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: host_sex_enum\n host_shape:\n name: host_shape\n annotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\n description: Morphological shape of host\n title: host shape\n examples:\n - value: round\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host shape\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000261\n multivalued: false\n alias: host_shape\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_subject_id:\n name: host_subject_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: A unique identifier by which each subject can be referred to, de-identified.\n title: host subject id\n examples:\n - value: MPI123\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subject id\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000861\n multivalued: false\n alias: host_subject_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_subspecf_genlin:\n name: host_subspecf_genlin\n annotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\n description: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n name and the lineage rank separated by a colon, e.g., biovar:abc123.\n title: host subspecific genetic lineage\n examples:\n - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subspecific genetic lineage\n rank: 1000\n is_a: core field\n string_serialization: '{rank name}:{text}'\n slot_uri: MIXS:0001318\n multivalued: true\n alias: host_subspecf_genlin\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_substrate:\n name: host_substrate\n annotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\n description: The growth substrate of the host.\n title: host substrate\n examples:\n - value: rock\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host substrate\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000252\n multivalued: false\n alias: host_substrate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n host_symbiont:\n name: host_symbiont\n annotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\n description: The taxonomic name of the organism(s) found living in mutualistic,\n commensalistic, or parasitic symbiosis with the specific host.\n title: observed host symbionts\n examples:\n - value: flukeworms\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed host symbionts\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001298\n multivalued: true\n alias: host_symbiont\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n host_tot_mass:\n name: host_tot_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Total mass of the host at collection, the unit depends on host\n title: host total mass\n examples:\n - value: 2500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host total mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000263\n multivalued: false\n alias: host_tot_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n host_wet_mass:\n name: host_wet_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of wet mass\n title: host wet mass\n examples:\n - value: 1500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host wet mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000567\n multivalued: false\n alias: host_wet_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n humidity:\n name: humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of water vapour in the air, at the time of sampling\n title: humidity\n examples:\n - value: 25 gram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000100\n multivalued: false\n alias: humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n humidity_regm:\n name: humidity_regm\n annotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying degree\n of humidity; information about treatment involving use of growth hormones; should\n include amount of humidity administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\n title: humidity regimen\n examples:\n - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000568\n multivalued: true\n alias: humidity_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n indoor_space:\n name: indoor_space\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A distinguishable space within a structure, the purpose for which\n discrete areas of a building is used\n title: indoor space\n examples:\n - value: foyer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor space\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000763\n multivalued: false\n alias: indoor_space\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_space_enum\n indoor_surf:\n name: indoor_surf\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of indoor surface\n title: indoor surface\n examples:\n - value: wall\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor surface\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000764\n multivalued: false\n alias: indoor_surf\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_surf_enum\n indust_eff_percent:\n name: indust_eff_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of industrial effluents received by wastewater treatment\n plant\n title: industrial effluent percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - industrial effluent percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000662\n multivalued: false\n alias: indust_eff_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n inorg_particles:\n name: inorg_particles\n annotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\n title: inorganic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inorganic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000664\n multivalued: true\n alias: inorg_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n inside_lux:\n name: inside_lux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded value at sampling time (power density)\n title: inside lux light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inside lux light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000168\n multivalued: false\n alias: inside_lux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n int_wall_cond:\n name: int_wall_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the wall at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: interior wall condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - interior wall condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000813\n multivalued: false\n alias: int_wall_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: int_wall_cond_enum\n investigation field:\n name: investigation field\n description: field describing aspect of the investigation/study to which the sample\n belongs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: investigation_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n iw_bt_date_well:\n name: iw_bt_date_well\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Injection water breakthrough date per well following a secondary\n and/or tertiary recovery\n title: injection water breakthrough date of specific well\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water breakthrough date of specific well\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001010\n multivalued: false\n alias: iw_bt_date_well\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n iwf:\n name: iwf\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Proportion of the produced fluids derived from injected water at\n the time of sampling. (e.g. 87%)\n title: injection water fraction\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water fraction\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000455\n multivalued: false\n alias: iwf\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n last_clean:\n name: last_clean\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The last time the floor was cleaned (swept, mopped, vacuumed)\n title: last time swept/mopped/vacuumed\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - last time swept/mopped/vacuumed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000814\n multivalued: false\n alias: last_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n lat_lon:\n name: lat_lon\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n todos:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n multivalued: false\n alias: lat_lon\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n lbc_thirty:\n name: lbc_thirty\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined after 30 minute incubation\n title: lime buffer capacity (at 30 minutes)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 543 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n aliases:\n - lbc_thirty\n - lbc30\n - lime buffer capacity (at 30 minutes)\n rank: 1000\n is_a: attribute\n alias: lbc_thirty\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n lbceq:\n name: lbceq\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined at equilibrium after 5 day incubation\n title: lime buffer capacity (after 5 day incubation)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 1575 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - lbceq\n - lime buffer capacity (at 5-day equilibrium)\n rank: 1000\n is_a: attribute\n alias: lbceq\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_intensity:\n name: light_intensity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of light intensity\n title: light intensity\n examples:\n - value: 0.3 lux\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light intensity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000706\n multivalued: false\n alias: light_intensity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_regm:\n name: light_regm\n annotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\n title: light regimen\n examples:\n - value: incandescant light;10 lux;450 nanometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000569\n multivalued: false\n alias: light_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n light_type:\n name: light_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Application of light to achieve some practical or aesthetic effect.\n Lighting includes the use of both artificial light sources such as lamps and\n light fixtures, as well as natural illumination by capturing daylight. Can also\n include absence of light\n title: light type\n examples:\n - value: desk lamp\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000769\n multivalued: true\n alias: light_type\n owner: Biosample\n domain_of:\n - Biosample\n range: light_type_enum\n link_addit_analys:\n name: link_addit_analys\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to additional analysis results performed on the sample\n title: links to additional analysis\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - links to additional analysis\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000340\n multivalued: false\n alias: link_addit_analys\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n link_class_info:\n name: link_class_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to digitized soil maps or other soil classification information\n title: link to classification information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to classification information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000329\n multivalued: false\n alias: link_class_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n link_climate_info:\n name: link_climate_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to climate resource\n title: link to climate information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to climate information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000328\n multivalued: false\n alias: link_climate_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n lithology:\n name: lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: lithology\n examples:\n - value: Volcanic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000990\n multivalued: false\n alias: lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: lithology_enum\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n multivalued: false\n alias: local_class\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n local_class_meth:\n name: local_class_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the local soil classification\n title: soil_taxonomic/local classification method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000331\n multivalued: false\n alias: local_class_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n magnesium:\n name: magnesium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per\n kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of magnesium in the sample\n title: magnesium\n examples:\n - value: 52.8 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - magnesium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000431\n multivalued: false\n alias: magnesium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n manganese:\n name: manganese\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of manganese in the sample\n title: manganese\n examples:\n - value: 24.7 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - manganese\n rank: 1000\n is_a: attribute\n alias: manganese\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n max_occup:\n name: max_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The maximum amount of people allowed in the indoor environment\n title: maximum occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - maximum occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000229\n multivalued: false\n alias: max_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mean_frict_vel:\n name: mean_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean friction velocity\n title: mean friction velocity\n examples:\n - value: 0.5 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000498\n multivalued: false\n alias: mean_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mean_peak_frict_vel:\n name: mean_peak_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean peak friction velocity\n title: mean peak friction velocity\n examples:\n - value: 1 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean peak friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000502\n multivalued: false\n alias: mean_peak_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mech_struc:\n name: mech_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'mechanical structure: a moving structure'\n title: mechanical structure\n examples:\n - value: elevator\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000815\n multivalued: false\n alias: mech_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: mech_struc_enum\n mechanical_damage:\n name: mechanical_damage\n annotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\n description: Information about any mechanical damage exerted on the plant; can\n include multiple damages and sites\n title: mechanical damage\n examples:\n - value: pruning;bark\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical damage\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0001052\n multivalued: true\n alias: mechanical_damage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n methane:\n name: methane\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Methane (gas) amount or concentration at the time of sampling\n title: methane\n examples:\n - value: 1800 parts per billion\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - methane\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000101\n multivalued: false\n alias: methane\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n micro_biomass_meth:\n name: micro_biomass_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining microbial biomass\n title: microbial biomass method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000339\n multivalued: false\n alias: micro_biomass_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n microbial_biomass:\n name: microbial_biomass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n to have correction factors used for conversion to the final units\n title: microbial biomass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000650\n multivalued: false\n alias: microbial_biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n mineral_nutr_regm:\n name: mineral_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n mineral nutrient regimens\n title: mineral nutrient regimen\n examples:\n - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000570\n multivalued: true\n alias: mineral_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n misc_param:\n name: misc_param\n annotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Any other measurement performed or parameter collected, that is not\n listed here\n title: miscellaneous parameter\n examples:\n - value: Bicarbonate ion concentration;2075 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - miscellaneous parameter\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000752\n multivalued: true\n alias: misc_param\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n n_alkanes:\n name: n_alkanes\n annotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of n-alkanes; can include multiple n-alkanes\n title: n-alkanes\n examples:\n - value: n-hexadecane;100 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - n-alkanes\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000503\n multivalued: true\n alias: n_alkanes\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n nitrate:\n name: nitrate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate in the sample\n title: nitrate\n examples:\n - value: 65 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000425\n multivalued: false\n alias: nitrate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrate_nitrogen:\n name: nitrate_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate nitrogen in the sample\n title: nitrate_nitrogen\n comments:\n - often below some specified limit of detection\n examples:\n - value: 0.29 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrate_nitrogen\n - NO3-N\n rank: 1000\n is_a: attribute\n alias: nitrate_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite:\n name: nitrite\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite in the sample\n title: nitrite\n examples:\n - value: 0.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000426\n multivalued: false\n alias: nitrite\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite_nitrogen:\n name: nitrite_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite nitrogen in the sample\n title: nitrite_nitrogen\n examples:\n - value: 1.2 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrite_nitrogen\n - NO2-N\n rank: 1000\n is_a: attribute\n alias: nitrite_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitro:\n name: nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrogen (total)\n title: nitrogen\n examples:\n - value: 4.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000504\n multivalued: false\n alias: nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n non_min_nutr_regm:\n name: non_min_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple non-mineral nutrient regimens\n title: non-mineral nutrient regimen\n examples:\n - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - non-mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000571\n multivalued: true\n alias: non_min_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n multivalued: false\n alias: nucl_acid_amp\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucl_acid_ext:\n name: nucl_acid_ext\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the material separation to recover\n the nucleic acid fraction from a sample\n title: nucleic acid extraction\n examples:\n - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid extraction\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000037\n multivalued: false\n alias: nucl_acid_ext\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucleic acid sequence source field:\n name: nucleic acid sequence source field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: nucleic_acid_sequence_source_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n number_pets:\n name: number_pets\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of pets residing in the sampled space\n title: number of pets\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of pets\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000231\n multivalued: false\n alias: number_pets\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n number_plants:\n name: number_plants\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of plant(s) in the sampling space\n title: number of houseplants\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of houseplants\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000230\n multivalued: false\n alias: number_plants\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n number_resident:\n name: number_resident\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of individuals currently occupying in the sampling location\n title: number of residents\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of residents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000232\n multivalued: false\n alias: number_resident\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n occup_density_samp:\n name: occup_density_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Average number of occupants at time of sampling per square footage\n title: occupant density at sampling\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupant density at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000217\n multivalued: false\n alias: occup_density_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n occup_document:\n name: occup_document\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of documentation of occupancy\n title: occupancy documentation\n examples:\n - value: estimate\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy documentation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000816\n multivalued: false\n alias: occup_document\n owner: Biosample\n domain_of:\n - Biosample\n range: occup_document_enum\n occup_samp:\n name: occup_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of occupants present at time of sample within the given space\n title: occupancy at sampling\n examples:\n - value: '10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000772\n multivalued: false\n alias: occup_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_carb:\n name: org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic carbon\n title: organic carbon\n examples:\n - value: 1.5 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000508\n multivalued: false\n alias: org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_count_qpcr_info:\n name: org_count_qpcr_info\n annotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\n description: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\n title: organism count qPCR information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count qPCR information\n rank: 1000\n is_a: core field\n string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\n slot_uri: MIXS:0000099\n multivalued: false\n alias: org_count_qpcr_info\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n org_matter:\n name: org_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic matter\n title: organic matter\n examples:\n - value: 1.75 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000204\n multivalued: false\n alias: org_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_nitro:\n name: org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic nitrogen\n title: organic nitrogen\n examples:\n - value: 4 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000205\n multivalued: false\n alias: org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n org_particles:\n name: org_particles\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\n title: organic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000665\n multivalued: true\n alias: org_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n organism_count:\n name: organism_count\n annotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\n description: 'Total cell count of any organism (or group of organisms) per gram,\n volume or area of sample, should include name of organism followed by count.\n The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n title: organism count\n examples:\n - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000103\n multivalued: true\n alias: organism_count\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n owc_tvdss:\n name: owc_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n title: oil water contact depth\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oil water contact depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000405\n multivalued: false\n alias: owc_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n oxy_stat_samp:\n name: oxy_stat_samp\n description: Oxygenation status of sample\n title: oxygenation status of sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000753\n multivalued: false\n alias: oxy_stat_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n oxygen:\n name: oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygen (gas) amount or concentration at the time of sampling\n title: oxygen\n examples:\n - value: 600 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000104\n multivalued: false\n alias: oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n part_org_carb:\n name: part_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic carbon\n title: particulate organic carbon\n examples:\n - value: 1.92 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000515\n multivalued: false\n alias: part_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n part_org_nitro:\n name: part_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic nitrogen\n title: particulate organic nitrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000719\n multivalued: false\n alias: part_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n particle_class:\n name: particle_class\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\n description: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle\n preceded by the name of the particle type; can include multiple values\n title: particle classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particle classification\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000206\n multivalued: true\n alias: particle_class\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n multivalued: false\n alias: pcr_cond\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n multivalued: false\n alias: pcr_primers\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n permeability:\n name: permeability\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n title: permeability\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - permeability\n rank: 1000\n is_a: core field\n string_serialization: '{integer} - {integer} {unit}'\n slot_uri: MIXS:0000404\n multivalued: false\n alias: permeability\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n perturbation:\n name: perturbation\n annotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time\n of the entire perturbation period; can include multiple perturbation types\n title: perturbation\n examples:\n - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - perturbation\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000754\n multivalued: true\n alias: perturbation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pesticide_regm:\n name: pesticide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of insecticides; should\n include the name of pesticide, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple pesticide\n regimens\n title: pesticide regimen\n examples:\n - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pesticide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000573\n multivalued: true\n alias: pesticide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n petroleum_hydrocarb:\n name: petroleum_hydrocarb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of petroleum hydrocarbon\n title: petroleum hydrocarbon\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - petroleum hydrocarbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000516\n multivalued: false\n alias: petroleum_hydrocarb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ph:\n name: ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\n title: pH\n examples:\n - value: '7.2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001001\n multivalued: false\n alias: ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n ph_meth:\n name: ph_meth\n description: Reference or method used in determining ph\n title: pH method\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001106\n multivalued: false\n alias: ph_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n ph_regm:\n name: ph_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plants to varying\n levels of ph of the growth media, treatment regimen including how many times\n the treatment was repeated, how long each treatment lasted, and the start and\n end time of the entire treatment; can include multiple regimen\n title: pH regimen\n examples:\n - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001056\n multivalued: true\n alias: ph_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n phaeopigments:\n name: phaeopigments\n annotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phaeopigments; can include multiple phaeopigments\n title: phaeopigments\n examples:\n - value: 2.5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phaeopigments\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000180\n multivalued: true\n alias: phaeopigments\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n phosphate:\n name: phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of phosphate\n title: phosphate\n examples:\n - value: 0.7 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000505\n multivalued: false\n alias: phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n phosplipid_fatt_acid:\n name: phosplipid_fatt_acid\n annotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phospholipid fatty acids; can include multiple values\n title: phospholipid fatty acid\n examples:\n - value: 2.98 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phospholipid fatty acid\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000181\n multivalued: true\n alias: phosplipid_fatt_acid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n photon_flux:\n name: photon_flux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of photon flux\n title: photon flux\n examples:\n - value: 3.926 micromole photons per second per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - photon flux\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000725\n multivalued: false\n alias: photon_flux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n plant_growth_med:\n name: plant_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n vitro liquid culture medium. Recommended value is a specific value from EO:plant\n growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n or other controlled vocabulary\n title: plant growth medium\n examples:\n - value: hydroponic plant culture media [EO:0007067]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant growth medium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001057\n multivalued: false\n alias: plant_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n plant_product:\n name: plant_product\n annotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the plant, where the sample was obtained from\n title: plant product\n examples:\n - value: xylem sap [PO:0025539]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant product\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001058\n multivalued: false\n alias: plant_product\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n plant_sex:\n name: plant_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n staminate, monoecieous, hermaphrodite.\n title: plant sex\n examples:\n - value: Hermaphroditic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001059\n multivalued: false\n alias: plant_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: plant_sex_enum\n plant_struc:\n name: plant_struc\n annotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n sex of it can be recorded here.\n title: plant structure\n examples:\n - value: epidermis [PO:0005679]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant structure\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0001060\n multivalued: false\n alias: plant_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n pollutants:\n name: pollutants\n annotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Pollutant types and, amount or concentrations measured at the time\n of sampling; can report multiple pollutants by entering numeric values preceded\n by name of pollutant\n title: pollutants\n examples:\n - value: lead;0.15 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pollutants\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000107\n multivalued: true\n alias: pollutants\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pool_dna_extracts:\n name: pool_dna_extracts\n annotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\n description: Indicate whether multiple DNA extractions were mixed. If the answer\n yes, the number of extracts that were pooled should be given\n title: pooling of DNA extracts (if done)\n examples:\n - value: yes;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pooling of DNA extracts (if done)\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{integer}'\n slot_uri: MIXS:0000325\n multivalued: false\n alias: pool_dna_extracts\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n porosity:\n name: porosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Porosity of deposited sediment is volume of voids divided by the\n total volume of sample\n title: porosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - porosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000211\n multivalued: false\n alias: porosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n potassium:\n name: potassium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of potassium in the sample\n title: potassium\n examples:\n - value: 463 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - potassium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000430\n multivalued: false\n alias: potassium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n pour_point:\n name: pour_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n a high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n title: pour point\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pour point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000127\n multivalued: false\n alias: pour_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n pre_treatment:\n name: pre_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process of pre-treatment removes materials that can be easily\n collected from the raw wastewater\n title: pre-treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pre-treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000348\n multivalued: false\n alias: pre_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n pres_animal_insect:\n name: pres_animal_insect\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\n description: The type and number of animals or insects present in the sampling\n space.\n title: presence of pets, animals, or insects\n examples:\n - value: cat;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - presence of pets, animals, or insects\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000819\n multivalued: false\n alias: pres_animal_insect\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n pattern: ^(cat|dog|rodent|snake|other);\\d+$\n pressure:\n name: pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\n description: Pressure to which the sample is subject to, in atmospheres\n title: pressure\n examples:\n - value: 50 atmosphere\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000412\n multivalued: false\n alias: pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n prev_land_use_meth:\n name: prev_land_use_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining previous land use and dates\n title: history/previous land use method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000316\n multivalued: false\n alias: prev_land_use_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n previous_land_use:\n name: previous_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\n description: Previous land use and dates\n title: history/previous land use\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use\n rank: 1000\n is_a: core field\n string_serialization: '{text};{timestamp}'\n slot_uri: MIXS:0000315\n multivalued: false\n alias: previous_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n primary_prod:\n name: primary_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of primary production, generally measured as isotope\n uptake\n title: primary production\n examples:\n - value: 100 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000728\n multivalued: false\n alias: primary_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n primary_treatment:\n name: primary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process to produce both a generally homogeneous liquid capable\n of being treated biologically and a sludge that can be separately treated or\n processed\n title: primary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000349\n multivalued: false\n alias: primary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n prod_rate:\n name: prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n title: production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000452\n multivalued: false\n alias: prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n prod_start_date:\n name: prod_start_date\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Date of field's first production\n title: production start date\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001008\n multivalued: false\n alias: prod_start_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n profile_position:\n name: profile_position\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\n title: profile position\n examples:\n - value: summit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - profile position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001084\n multivalued: false\n alias: profile_position\n owner: Biosample\n domain_of:\n - Biosample\n range: profile_position_enum\n quad_pos:\n name: quad_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The quadrant position of the sampling room within the building\n title: quadrant position\n examples:\n - value: West side\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - quadrant position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000820\n multivalued: false\n alias: quad_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: quad_pos_enum\n radiation_regm:\n name: radiation_regm\n annotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plant or a plant\n part to a particular radiation regimen; should include the radiation type, amount\n or intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple radiation regimens\n title: radiation regimen\n examples:\n - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - radiation regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000575\n multivalued: true\n alias: radiation_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n rainfall_regm:\n name: rainfall_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to a given amount\n of rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\n title: rainfall regimen\n examples:\n - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rainfall regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000576\n multivalued: true\n alias: rainfall_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n reactor_type:\n name: reactor_type\n annotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Anaerobic digesters can be designed and engineered to operate using\n a number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\n title: reactor type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reactor type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000350\n multivalued: false\n alias: reactor_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n redox_potential:\n name: redox_potential\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\n description: Redox potential, measured relative to a hydrogen cell, indicating\n oxidation or reduction potential\n title: redox potential\n examples:\n - value: 300 millivolt\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - redox potential\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000182\n multivalued: false\n alias: redox_potential\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_air_humidity:\n name: rel_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Partial vapor and air pressure, density of the vapor and air, or\n by the actual mass of the vapor and air\n title: relative air humidity\n examples:\n - value: 80%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000121\n multivalued: false\n alias: rel_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_humidity_out:\n name: rel_humidity_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded outside relative humidity value at the time of sampling\n title: outside relative humidity\n examples:\n - value: 12 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - outside relative humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000188\n multivalued: false\n alias: rel_humidity_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n rel_samp_loc:\n name: rel_samp_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The sampling location within the train car\n title: relative sampling location\n examples:\n - value: center of car\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative sampling location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000821\n multivalued: false\n alias: rel_samp_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: rel_samp_loc_enum\n reservoir:\n name: reservoir\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the reservoir (e.g. Carapebus)\n title: reservoir name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reservoir name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000303\n multivalued: false\n alias: reservoir\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n resins_pc:\n name: resins_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: resins wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - resins wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000134\n multivalued: false\n alias: resins_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_air_exch_rate:\n name: room_air_exch_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The rate at which outside air replaces indoor air in a given space\n title: room air exchange rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room air exchange rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000169\n multivalued: false\n alias: room_air_exch_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n room_architec_elem:\n name: room_architec_elem\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\n title: room architectural elements\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room architectural elements\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000233\n multivalued: false\n alias: room_architec_elem\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n room_condt:\n name: room_condt\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The condition of the room at the time of sampling\n title: room condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000822\n multivalued: false\n alias: room_condt\n owner: Biosample\n domain_of:\n - Biosample\n range: room_condt_enum\n room_connected:\n name: room_connected\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms connected to the sampling room by a doorway\n title: rooms connected by a doorway\n examples:\n - value: office\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms connected by a doorway\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000826\n multivalued: false\n alias: room_connected\n owner: Biosample\n domain_of:\n - Biosample\n range: room_connected_enum\n room_count:\n name: room_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of rooms in the built structure including all room\n types\n title: room count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000234\n multivalued: false\n alias: room_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_dim:\n name: room_dim\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length, width and height of sampling room\n title: room dimensions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room dimensions\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n slot_uri: MIXS:0000192\n multivalued: false\n alias: room_dim\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_door_dist:\n name: room_door_dist\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Distance between doors (meters) in the hallway between the sampling\n room and adjacent rooms\n title: room door distance\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room door distance\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000193\n multivalued: false\n alias: room_door_dist\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_door_share:\n name: room_door_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a door with the\n sampling room\n title: rooms that share a door with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a door with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000242\n multivalued: false\n alias: room_door_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_hallway:\n name: room_hallway\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) located in the same hallway\n as sampling room\n title: rooms that are on the same hallway\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that are on the same hallway\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000238\n multivalued: false\n alias: room_hallway\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_loc:\n name: room_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The position of the room within the building\n title: room location in building\n examples:\n - value: interior room\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room location in building\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000823\n multivalued: false\n alias: room_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: room_loc_enum\n room_moist_dam_hist:\n name: room_moist_dam_hist\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\n title: room moisture damage or mold history\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room moisture damage or mold history\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000235\n multivalued: false\n alias: room_moist_dam_hist\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n room_net_area:\n name: room_net_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The net floor area of sampling room. Net area excludes wall thicknesses\n title: room net area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room net area\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000194\n multivalued: false\n alias: room_net_area\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_occup:\n name: room_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Count of room occupancy at time of sampling\n title: room occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000236\n multivalued: false\n alias: room_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n room_samp_pos:\n name: room_samp_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal sampling position in the room relative to architectural\n elements\n title: room sampling position\n examples:\n - value: south corner\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room sampling position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000824\n multivalued: false\n alias: room_samp_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: room_samp_pos_enum\n room_type:\n name: room_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The main purpose or activity of the sampling room. A room is any\n distinguishable space within a structure\n title: room type\n examples:\n - value: bathroom\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000825\n multivalued: false\n alias: room_type\n owner: Biosample\n domain_of:\n - Biosample\n range: room_type_enum\n room_vol:\n name: room_vol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Volume of sampling room\n title: room volume\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room volume\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000195\n multivalued: false\n alias: room_vol\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_wall_share:\n name: room_wall_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a wall with the\n sampling room\n title: rooms that share a wall with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a wall with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000243\n multivalued: false\n alias: room_wall_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n room_window_count:\n name: room_window_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of windows in the room\n title: room window count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room window count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000237\n multivalued: false\n alias: room_window_count\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n root_cond:\n name: root_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\n title: rooting conditions\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001061\n multivalued: false\n alias: root_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_carbon:\n name: root_med_carbon\n annotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n title: rooting medium carbon\n examples:\n - value: sucrose\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium carbon\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000577\n multivalued: false\n alias: root_med_carbon\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_macronutr:\n name: root_med_macronutr\n annotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium macronutrients (N,P, K,\n Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n title: rooting medium macronutrients\n examples:\n - value: KH2PO4;170\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium macronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000578\n multivalued: false\n alias: root_med_macronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_micronutr:\n name: root_med_micronutr\n annotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n title: rooting medium micronutrients\n examples:\n - value: H3BO3;6.2\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium micronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000579\n multivalued: false\n alias: root_med_micronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_ph:\n name: root_med_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: pH measurement of the culture rooting medium; e.g. 5.5.\n title: rooting medium pH\n examples:\n - value: '7.5'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001062\n multivalued: false\n alias: root_med_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n root_med_regl:\n name: root_med_regl\n annotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Growth regulators in the culture rooting medium such as cytokinins,\n auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n title: rooting medium regulators\n examples:\n - value: abscisic acid;0.75 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium regulators\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000581\n multivalued: false\n alias: root_med_regl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_solid:\n name: root_med_solid\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\n title: rooting medium solidifier\n examples:\n - value: agar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium solidifier\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001063\n multivalued: false\n alias: root_med_solid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n root_med_suppl:\n name: root_med_suppl\n annotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\n title: rooting medium organic supplements\n examples:\n - value: nicotinic acid;0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium organic supplements\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000580\n multivalued: false\n alias: root_med_suppl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n salinity:\n name: salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The total concentration of all dissolved salts in a liquid or solid\n sample. While salinity can be measured by a complete chemical analysis, this\n method is difficult and time consuming. More often, it is instead derived from\n the conductivity measurement. This is known as practical salinity. These derivations\n compare the specific conductance of the sample to a salinity standard such as\n seawater.\n title: salinity\n examples:\n - value: 25 practical salinity unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000183\n multivalued: false\n alias: salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n salinity_meth:\n name: salinity_meth\n description: Reference or method used in determining salinity\n title: salinity method\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000341\n multivalued: false\n alias: salinity_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n salt_regm:\n name: salt_regm\n annotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of salts as supplement\n to liquid and soil growth media; should include the name of salt, amount administered,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple salt regimens\n title: salt regimen\n examples:\n - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salt regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000582\n multivalued: true\n alias: salt_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_capt_status:\n name: samp_capt_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Reason for the sample\n title: sample capture status\n examples:\n - value: farm sample\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample capture status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000860\n multivalued: false\n alias: samp_capt_status\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_capt_status_enum\n samp_collec_device:\n name: samp_collec_device\n annotations:\n expected_value:\n tag: expected_value\n value: device name\n description: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n title: sample collection device\n examples:\n - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection device\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000002\n multivalued: false\n alias: samp_collec_device\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n samp_collec_method:\n name: samp_collec_method\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\n description: The method employed for collecting the sample.\n title: sample collection method\n examples:\n - value: swabbing\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection method\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001225\n multivalued: false\n alias: samp_collec_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n samp_collect_point:\n name: samp_collect_point\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry\n in \"additional info\" field\n title: sample collection point\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001015\n multivalued: false\n alias: samp_collect_point\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_collect_point_enum\n samp_dis_stage:\n name: samp_dis_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\n title: sample disease stage\n examples:\n - value: infection\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample disease stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000249\n multivalued: false\n alias: samp_dis_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_dis_stage_enum\n samp_floor:\n name: samp_floor\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor of the building, where the sampling room is located\n title: sampling floor\n examples:\n - value: 4th floor\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling floor\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000828\n multivalued: false\n alias: samp_floor\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_floor_enum\n samp_loc_corr_rate:\n name: samp_loc_corr_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\n description: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short\n term rates and for that reason they are preferred during reporting. In the case\n of suspected MIC, corrosion rate measurements at the time of sampling might\n provide insights into the involvement of certain microbial community members\n in MIC as well as potential microbial interplays\n title: corrosion rate at sample location\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - corrosion rate at sample location\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000136\n multivalued: false\n alias: samp_loc_corr_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_mat_process:\n name: samp_mat_process\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A brief description of any processing applied to the sample during\n or after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\n title: sample material processing\n examples:\n - value: filtering of seawater, storing samples in ethanol\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample material processing\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000016\n multivalued: false\n alias: samp_mat_process\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n samp_md:\n name: samp_md\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: In non deviated well, measured depth is equal to the true vertical\n depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n wells, the MD is the length of trajectory of the borehole measured from the\n same reference or datum. Common datums used are ground level (GL), drilling\n rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: sample measured depth\n examples:\n - value: 1534 meter;MSL\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample measured depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000413\n multivalued: false\n alias: samp_md\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_preserv:\n name: samp_preserv\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\n description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n title: preservative added to sample\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - preservative added to sample\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000463\n multivalued: false\n alias: samp_preserv\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_room_id:\n name: samp_room_id\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\n title: sampling room ID or name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling room ID or name\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000244\n multivalued: false\n alias: samp_room_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_size:\n name: samp_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample collected.\n title: amount or size of sample collected\n examples:\n - value: 5 liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount or size of sample collected\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000001\n multivalued: false\n alias: samp_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_sort_meth:\n name: samp_sort_meth\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\n description: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers\n in diameter, where common values of X would be 10 and 2.5 full size sorting\n in a cascade impactor.\n title: sample size sorting method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample size sorting method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000216\n multivalued: true\n alias: samp_sort_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_dur:\n name: samp_store_dur\n annotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Duration for which the sample was stored\n title: sample storage duration\n examples:\n - value: P1Y6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage duration\n rank: 1000\n is_a: core field\n string_serialization: '{duration}'\n slot_uri: MIXS:0000116\n multivalued: false\n alias: samp_store_dur\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_loc:\n name: samp_store_loc\n annotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\n description: Location at which sample was stored, usually name of a specific freezer/room\n title: sample storage location\n examples:\n - value: Freezer no:5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage location\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000755\n multivalued: false\n alias: samp_store_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_store_temp:\n name: samp_store_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature at which sample was stored, e.g. -80 degree Celsius\n title: sample storage temperature\n examples:\n - value: -80 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000110\n multivalued: false\n alias: samp_store_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n samp_subtype:\n name: samp_subtype\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n please propose entry in \"additional info\" field\n title: sample subtype\n examples:\n - value: biofilm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample subtype\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000999\n multivalued: false\n alias: samp_subtype\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_subtype_enum\n samp_taxon_id:\n name: samp_taxon_id\n annotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\n description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\n sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n 'blank sample' for negative controls.\n title: Taxonomy ID of DNA sample\n comments:\n - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Taxonomy ID of DNA sample\n rank: 1000\n is_a: investigation field\n slot_uri: MIXS:0001320\n multivalued: false\n alias: samp_taxon_id\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n samp_time_out:\n name: samp_time_out\n annotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The recent and long term history of outside sampling\n title: sampling time outside\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling time outside\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000196\n multivalued: false\n alias: samp_time_out\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_transport_cond:\n name: samp_transport_cond\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n title: sample transport conditions\n examples:\n - value: 5 days;-20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample transport conditions\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000410\n multivalued: false\n alias: samp_transport_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_tvdss:\n name: samp_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\n title: sample true vertical depth subsea\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample true vertical depth subsea\n rank: 1000\n is_a: core field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000409\n multivalued: false\n alias: samp_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_type:\n name: samp_type\n annotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material from which the sample was obtained. For the\n Hydrocarbon package, samples include types like core, rock trimmings, drill\n cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n produced water, injected water, swabs, etc. For the Food Package, samples are\n usually categorized as food, body products or tissues, or environmental material.\n This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n title: sample type\n examples:\n - value: built environment sample [GENEPIO:0001248]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000998\n multivalued: false\n alias: samp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n samp_vol_we_dna_ext:\n name: samp_vol_we_dna_ext\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\n description: 'Volume (ml) or mass (g) of total collected sample processed for\n DNA extraction. Note: total sample collected should be entered under the term\n Sample Size (MIXS:0000001).'\n title: sample volume or weight for DNA extraction\n examples:\n - value: 1500 milliliter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample volume or weight for DNA extraction\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000111\n multivalued: false\n alias: samp_vol_we_dna_ext\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: QuantityValue\n samp_weather:\n name: samp_weather\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The weather on the sampling day\n title: sampling day weather\n examples:\n - value: foggy\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling day weather\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000827\n multivalued: false\n alias: samp_weather\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_weather_enum\n samp_well_name:\n name: samp_well_name\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the well (e.g. BXA1123) where sample was taken\n title: sample well name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample well name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000296\n multivalued: false\n alias: samp_well_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n saturates_pc:\n name: saturates_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: saturates wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - saturates wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000131\n multivalued: false\n alias: saturates_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season:\n name: season\n annotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\n description: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms\n listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n title: season\n examples:\n - value: autumn [NCIT:C94733]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - season\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000829\n multivalued: false\n alias: season\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season_environment:\n name: season_environment\n annotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment\n title: seasonal environment\n examples:\n - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001068\n multivalued: true\n alias: season_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n season_precpt:\n name: season_precpt\n description: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: average seasonal precipitation\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000645\n multivalued: false\n alias: season_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n season_temp:\n name: season_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean seasonal temperature\n title: mean seasonal temperature\n examples:\n - value: 18 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000643\n multivalued: false\n alias: season_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n season_use:\n name: season_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The seasons the space is occupied\n title: seasonal use\n examples:\n - value: Winter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000830\n multivalued: false\n alias: season_use\n owner: Biosample\n domain_of:\n - Biosample\n range: season_use_enum\n secondary_treatment:\n name: secondary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process for substantially degrading the biological content of\n the sewage\n title: secondary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000351\n multivalued: false\n alias: secondary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n sediment_type:\n name: sediment_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about the sediment type based on major constituents\n title: sediment type\n examples:\n - value: biogenous\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sediment type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001078\n multivalued: false\n alias: sediment_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sediment_type_enum\n seq_meth:\n name: seq_meth\n annotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\n description: Sequencing machine used. Where possible the term should be taken\n from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\n title: sequencing method\n examples:\n - value: 454 Genome Sequencer FLX [OBI:0000702]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequencing method\n rank: 1000\n is_a: sequencing field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000050\n multivalued: false\n alias: seq_meth\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n seq_quality_check:\n name: seq_quality_check\n annotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\n description: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or\n chromatograms). Applied only for sequences that are not submitted to SRA,ENA\n or DRA\n title: sequence quality check\n examples:\n - value: none\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequence quality check\n rank: 1000\n is_a: sequencing field\n string_serialization: '[none|manually edited]'\n slot_uri: MIXS:0000051\n multivalued: false\n alias: seq_quality_check\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n sequencing field:\n name: sequencing field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: sequencing_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sewage_type:\n name: sewage_type\n annotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of wastewater treatment plant as municipial or industrial\n title: sewage type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sewage type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000215\n multivalued: false\n alias: sewage_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shad_dev_water_mold:\n name: shad_dev_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the shading device\n title: shading device signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000834\n multivalued: false\n alias: shad_dev_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n shading_device_cond:\n name: shading_device_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the shading device at the time of sampling\n title: shading device condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000831\n multivalued: false\n alias: shading_device_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_cond_enum\n shading_device_loc:\n name: shading_device_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of the shading device in relation to the built structure\n title: shading device location\n examples:\n - value: exterior\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device location\n rank: 1000\n is_a: core field\n string_serialization: '[exterior|interior]'\n slot_uri: MIXS:0000832\n multivalued: false\n alias: shading_device_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shading_device_mat:\n name: shading_device_mat\n annotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the shading device is composed of\n title: shading device material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device material\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000245\n multivalued: false\n alias: shading_device_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n shading_device_type:\n name: shading_device_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of shading device\n title: shading device type\n examples:\n - value: slatted aluminum awning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000835\n multivalued: false\n alias: shading_device_type\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_type_enum\n sieving:\n name: sieving\n description: Collection design of pooled samples and/or sieve size and amount\n of sample sieved\n title: composite design/sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n slot_uri: MIXS:0000322\n multivalued: false\n alias: sieving\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n silicate:\n name: silicate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of silicate\n title: silicate\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - silicate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000184\n multivalued: false\n alias: silicate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n size_frac:\n name: size_frac\n annotations:\n expected_value:\n tag: expected_value\n value: filter size value range\n description: Filtering pore size used in sample preparation\n title: size fraction selected\n examples:\n - value: 0-0.22 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size fraction selected\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000017\n multivalued: false\n alias: size_frac\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n size_frac_low:\n name: size_frac_low\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\n title: size-fraction lower threshold\n examples:\n - value: 0.2 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction lower threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000735\n multivalued: false\n alias: size_frac_low\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n size_frac_up:\n name: size_frac_up\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to retain the sample. Materials\n smaller than the size threshold are excluded from the sample\n title: size-fraction upper threshold\n examples:\n - value: 20 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction upper threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000736\n multivalued: false\n alias: size_frac_up\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). - This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n title: slope aspect\n todos:\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000647\n multivalued: false\n alias: slope_aspect\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n slope_gradient:\n name: slope_gradient\n description: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This\n measure is usually taken with a hand level meter or clinometer\n title: slope gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000646\n multivalued: false\n alias: slope_gradient\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sludge_retent_time:\n name: sludge_retent_time\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\n description: The time activated sludge remains in reactor\n title: sludge retention time\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sludge retention time\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000669\n multivalued: false\n alias: sludge_retent_time\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sodium:\n name: sodium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Sodium concentration in the sample\n title: sodium\n examples:\n - value: 10.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sodium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000428\n multivalued: false\n alias: sodium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soil_horizon:\n name: soil_horizon\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specific layer in the land area which measures parallel to the soil\n surface and possesses physical characteristics which differ from the layers\n above and beneath\n title: soil horizon\n examples:\n - value: A horizon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001082\n multivalued: false\n alias: soil_horizon\n owner: Biosample\n domain_of:\n - Biosample\n range: soil_horizon_enum\n soil_text_measure:\n name: soil_text_measure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to\n 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n clay loam) optional.\n title: soil texture measurement\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture measurement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000335\n multivalued: false\n alias: soil_text_measure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soil_texture_meth:\n name: soil_texture_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil texture\n title: soil texture method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000336\n multivalued: false\n alias: soil_texture_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n multivalued: false\n alias: soil_type\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n soil_type_meth:\n name: soil_type_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil series name or other\n lower-level classification\n title: soil type method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000334\n multivalued: false\n alias: soil_type_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n solar_irradiance:\n name: solar_irradiance\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per\n second\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\n title: solar irradiance\n examples:\n - value: 1.36 kilowatts per square meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solar irradiance\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000112\n multivalued: false\n alias: solar_irradiance\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n soluble_inorg_mat:\n name: soluble_inorg_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as ammonia, road-salt, sea-salt,\n cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n title: soluble inorganic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble inorganic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000672\n multivalued: true\n alias: soluble_inorg_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n soluble_org_mat:\n name: soluble_org_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\n title: soluble organic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble organic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000673\n multivalued: true\n alias: soluble_org_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n soluble_react_phosp:\n name: soluble_react_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of soluble reactive phosphorus\n title: soluble reactive phosphorus\n examples:\n - value: 0.1 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble reactive phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000738\n multivalued: false\n alias: soluble_react_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000026\n multivalued: false\n alias: source_mat_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n space_typ_state:\n name: space_typ_state\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal state of the space\n title: space typical state\n examples:\n - value: typically occupied\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - space typical state\n rank: 1000\n is_a: core field\n string_serialization: '[typically occupied|typically unoccupied]'\n slot_uri: MIXS:0000770\n multivalued: false\n alias: space_typ_state\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n specific:\n name: specific\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'The building specifications. If design is chosen, indicate phase:\n conceptual, schematic, design development, construction documents'\n title: specifications\n examples:\n - value: construction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specifications\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000836\n multivalued: false\n alias: specific\n owner: Biosample\n domain_of:\n - Biosample\n range: specific_enum\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n specific_humidity:\n name: specific_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n pound.\n title: specific humidity\n examples:\n - value: 15 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specific humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000214\n multivalued: false\n alias: specific_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sr_dep_env:\n name: sr_dep_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock depositional environment\n examples:\n - value: Marine\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000996\n multivalued: false\n alias: sr_dep_env\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_dep_env_enum\n sr_geol_age:\n name: sr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000997\n multivalued: false\n alias: sr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_geol_age_enum\n sr_kerog_type:\n name: sr_kerog_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock kerogen type\n examples:\n - value: Type IV\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock kerogen type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000994\n multivalued: false\n alias: sr_kerog_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_kerog_type_enum\n sr_lithology:\n name: sr_lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock lithology\n examples:\n - value: Coal\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000995\n multivalued: false\n alias: sr_lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_lithology_enum\n standing_water_regm:\n name: standing_water_regm\n annotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to standing water during a plant's\n life span, types can be flood water or standing water, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple regimens\n title: standing water regimen\n examples:\n - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - standing water regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001069\n multivalued: true\n alias: standing_water_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n store_cond:\n name: store_cond\n annotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Explain how and for how long the soil sample was stored before DNA\n extraction (fresh/frozen/other).\n title: storage conditions\n examples:\n - value: -20 degree Celsius freezer;P2Y10D\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - storage conditions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000327\n multivalued: false\n alias: store_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n substructure_type:\n name: substructure_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The substructure or under building is that largely hidden section\n of the building which is built off the foundations to the ground floor level\n title: substructure type\n examples:\n - value: basement\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - substructure type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000767\n multivalued: true\n alias: substructure_type\n owner: Biosample\n domain_of:\n - Biosample\n range: substructure_type_enum\n sulfate:\n name: sulfate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfate in the sample\n title: sulfate\n examples:\n - value: 5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000423\n multivalued: false\n alias: sulfate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sulfate_fw:\n name: sulfate_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original sulfate concentration in the hydrocarbon resource\n title: sulfate in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000407\n multivalued: false\n alias: sulfate_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n sulfide:\n name: sulfide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfide in the sample\n title: sulfide\n examples:\n - value: 2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000424\n multivalued: false\n alias: sulfide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_air_cont:\n name: surf_air_cont\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Contaminant identified on surface\n title: surface-air contaminant\n examples:\n - value: radon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface-air contaminant\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000759\n multivalued: true\n alias: surf_air_cont\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_air_cont_enum\n surf_humidity:\n name: surf_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Surfaces: water activity as a function of air and material moisture'\n title: surface humidity\n examples:\n - value: 10%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000123\n multivalued: false\n alias: surf_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_material:\n name: surf_material\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Surface materials at the point of sampling\n title: surface material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000758\n multivalued: false\n alias: surf_material\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_material_enum\n surf_moisture:\n name: surf_moisture\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Water held on a surface\n title: surface moisture\n examples:\n - value: 0.01 gram per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000128\n multivalued: false\n alias: surf_moisture\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n surf_moisture_ph:\n name: surf_moisture_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: ph measurement of surface\n title: surface moisture pH\n examples:\n - value: '7'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000760\n multivalued: false\n alias: surf_moisture_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n surf_temp:\n name: surf_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the surface at the time of sampling\n title: surface temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000125\n multivalued: false\n alias: surf_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n suspend_part_matter:\n name: suspend_part_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of suspended particulate matter\n title: suspended particulate matter\n examples:\n - value: 0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended particulate matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000741\n multivalued: false\n alias: suspend_part_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n suspend_solids:\n name: suspend_solids\n annotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n part per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances including a wide variety of material,\n such as silt, decaying plant and animal matter; can include multiple substances\n title: suspended solids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended solids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000150\n multivalued: true\n alias: suspend_solids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tan:\n name: tan\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n title: total acid number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total acid number\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000120\n multivalued: false\n alias: tan\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n multivalued: false\n alias: target_gene\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n multivalued: false\n alias: target_subfragment\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n temp:\n name: temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n description: Temperature of the sample at the time of sampling.\n title: temperature\n examples:\n - value: 25 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000113\n multivalued: false\n alias: temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n temp_out:\n name: temp_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded temperature value at sampling time outside\n title: temperature outside house\n examples:\n - value: 5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature outside house\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000197\n multivalued: false\n alias: temp_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tertiary_treatment:\n name: tertiary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process providing a final treatment stage to raise the effluent\n quality before it is discharged to the receiving environment\n title: tertiary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tertiary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000352\n multivalued: false\n alias: tertiary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tidal_stage:\n name: tidal_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of tide\n title: tidal stage\n examples:\n - value: high tide\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tidal stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000750\n multivalued: false\n alias: tidal_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: tidal_stage_enum\n tillage:\n name: tillage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Note method(s) used for tilling\n title: history/tillage\n examples:\n - value: chisel\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/tillage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001081\n multivalued: true\n alias: tillage\n owner: Biosample\n domain_of:\n - Biosample\n range: tillage_enum\n tiss_cult_growth_med:\n name: tiss_cult_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of plant tissue culture growth media used\n title: tissue culture growth media\n examples:\n - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tissue culture growth media\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001070\n multivalued: false\n alias: tiss_cult_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n toluene:\n name: toluene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of toluene in the sample\n title: toluene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - toluene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000154\n multivalued: false\n alias: toluene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_carb:\n name: tot_carb\n description: Total carbon content\n title: total carbon\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000525\n multivalued: false\n alias: tot_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_depth_water_col:\n name: tot_depth_water_col\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of total depth of water column\n title: total depth of water column\n examples:\n - value: 500 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total depth of water column\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000634\n multivalued: false\n alias: tot_depth_water_col\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_diss_nitro:\n name: tot_diss_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n title: total dissolved nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total dissolved nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000744\n multivalued: false\n alias: tot_diss_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_inorg_nitro:\n name: tot_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total inorganic nitrogen content\n title: total inorganic nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000745\n multivalued: false\n alias: tot_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_iron:\n name: tot_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total iron in the sample\n title: total iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000105\n multivalued: false\n alias: tot_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_nitro:\n name: tot_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\n title: total nitrogen concentration\n examples:\n - value: 50 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen concentration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000102\n multivalued: false\n alias: tot_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n description: Reference or method used in determining the total nitrogen\n title: total nitrogen content method\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000338\n multivalued: false\n alias: tot_nitro_cont_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n tot_nitro_content:\n name: tot_nitro_content\n description: Total nitrogen content of the sample\n title: total nitrogen content\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000530\n multivalued: false\n alias: tot_nitro_content\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_org_c_meth:\n name: tot_org_c_meth\n description: Reference or method used in determining total organic carbon\n title: total organic carbon method\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000337\n multivalued: false\n alias: tot_org_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n tot_org_carb:\n name: tot_org_carb\n description: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\n title: total organic carbon\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000533\n multivalued: false\n alias: tot_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_part_carb:\n name: tot_part_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total particulate carbon content\n title: total particulate carbon\n examples:\n - value: 35 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total particulate carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000747\n multivalued: false\n alias: tot_part_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_phosp:\n name: tot_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total phosphorus concentration in the sample, calculated by: total\n phosphorus = total dissolved phosphorus + particulate phosphorus'\n title: total phosphorus\n examples:\n - value: 0.03 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000117\n multivalued: false\n alias: tot_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_phosphate:\n name: tot_phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total amount or concentration of phosphate\n title: total phosphate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000689\n multivalued: false\n alias: tot_phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tot_sulfur:\n name: tot_sulfur\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total sulfur in the sample\n title: total sulfur\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total sulfur\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000419\n multivalued: false\n alias: tot_sulfur\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n train_line:\n name: train_line\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The subway line name\n title: train line\n examples:\n - value: red\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train line\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000837\n multivalued: false\n alias: train_line\n owner: Biosample\n domain_of:\n - Biosample\n range: train_line_enum\n train_stat_loc:\n name: train_stat_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train station collection location\n title: train station collection location\n examples:\n - value: forest hills\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train station collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000838\n multivalued: false\n alias: train_stat_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stat_loc_enum\n train_stop_loc:\n name: train_stop_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train stop collection location\n title: train stop collection location\n examples:\n - value: end\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train stop collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000839\n multivalued: false\n alias: train_stop_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stop_loc_enum\n turbidity:\n name: turbidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\n description: Measure of the amount of cloudiness or haziness in water caused by\n individual particles\n title: turbidity\n examples:\n - value: 0.3 nephelometric turbidity units\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - turbidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000191\n multivalued: false\n alias: turbidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tvdss_of_hcr_press:\n name: tvdss_of_hcr_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\n title: depth (TVDSS) of hydrocarbon resource pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000397\n multivalued: false\n alias: tvdss_of_hcr_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n tvdss_of_hcr_temp:\n name: tvdss_of_hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\n title: depth (TVDSS) of hydrocarbon resource temperature\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000394\n multivalued: false\n alias: tvdss_of_hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n typ_occup_density:\n name: typ_occup_density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal density of occupants\n title: typical occupant density\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - typical occupant density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000771\n multivalued: false\n alias: typ_occup_density\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n ventilation_rate:\n name: ventilation_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation rate of the system in the sampled premises\n title: ventilation rate\n examples:\n - value: 750 cubic meter per minute\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000114\n multivalued: false\n alias: ventilation_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n ventilation_type:\n name: ventilation_type\n annotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation system used in the sampled premises\n title: ventilation type\n examples:\n - value: Operable windows\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000756\n multivalued: false\n alias: ventilation_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n vfa:\n name: vfa\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of Volatile Fatty Acids in the sample\n title: volatile fatty acids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile fatty acids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000152\n multivalued: false\n alias: vfa\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n vfa_fw:\n name: vfa_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original volatile fatty acid concentration in the hydrocarbon resource\n title: vfa in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - vfa in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000408\n multivalued: false\n alias: vfa_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n vis_media:\n name: vis_media\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building visual media\n title: visual media\n examples:\n - value: 3D scans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - visual media\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000840\n multivalued: false\n alias: vis_media\n owner: Biosample\n domain_of:\n - Biosample\n range: vis_media_enum\n viscosity:\n name: viscosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n title: viscosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - viscosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000126\n multivalued: false\n alias: viscosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n volatile_org_comp:\n name: volatile_org_comp\n annotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of carbon-based chemicals that easily evaporate at\n room temperature; can report multiple volatile organic compounds by entering\n numeric values preceded by name of compound\n title: volatile organic compounds\n examples:\n - value: formaldehyde;500 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile organic compounds\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000115\n multivalued: true\n alias: volatile_org_comp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wall_area:\n name: wall_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The total area of the sampled room's walls\n title: wall area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000198\n multivalued: false\n alias: wall_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_const_type:\n name: wall_const_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building class of the wall defined by the composition of the\n building elements and fire-resistance rating.\n title: wall construction type\n examples:\n - value: fire resistive\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall construction type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000841\n multivalued: false\n alias: wall_const_type\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_const_type_enum\n wall_finish_mat:\n name: wall_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material utilized to finish the outer most layer of the wall\n title: wall finish material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000842\n multivalued: false\n alias: wall_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_finish_mat_enum\n wall_height:\n name: wall_height\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average height of the walls in the sampled room\n title: wall height\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000221\n multivalued: false\n alias: wall_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_loc:\n name: wall_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the wall within the room\n title: wall location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000843\n multivalued: false\n alias: wall_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_loc_enum\n wall_surf_treatment:\n name: wall_surf_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The surface treatment of interior wall\n title: wall surface treatment\n examples:\n - value: paneling\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall surface treatment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000845\n multivalued: false\n alias: wall_surf_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_surf_treatment_enum\n wall_texture:\n name: wall_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a wall surface\n title: wall texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000846\n multivalued: false\n alias: wall_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_texture_enum\n wall_thermal_mass:\n name: wall_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\n title: wall thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000222\n multivalued: false\n alias: wall_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n wall_water_mold:\n name: wall_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a wall\n title: wall signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000844\n multivalued: false\n alias: wall_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wastewater_type:\n name: wastewater_type\n annotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\n description: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\n title: wastewater type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wastewater type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000353\n multivalued: false\n alias: wastewater_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n water_cont_soil_meth:\n name: water_cont_soil_meth\n description: Reference or method used in determining the water content of soil\n title: water content method\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000323\n multivalued: false\n alias: water_cont_soil_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n description: Water content measurement\n title: water content\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - This is no longer matching the listed IRI from GSC. When NMDC has its own slots,\n map this to the MIxS slot\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000185\n multivalued: true\n alias: water_content\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n water_current:\n name: water_current\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of magnitude and direction of flow within a fluid\n title: water current\n examples:\n - value: 10 cubic meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water current\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000203\n multivalued: false\n alias: water_current\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_cut:\n name: water_cut\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\n title: water cut\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water cut\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000454\n multivalued: false\n alias: water_cut\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_feat_size:\n name: water_feat_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the water feature\n title: water feature size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000223\n multivalued: false\n alias: water_feat_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_feat_type:\n name: water_feat_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of water feature present within the building being sampled\n title: water feature type\n examples:\n - value: stream\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000847\n multivalued: false\n alias: water_feat_type\n owner: Biosample\n domain_of:\n - Biosample\n range: water_feat_type_enum\n water_prod_rate:\n name: water_prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Water production rates per well (e.g. 987 m3 / day)\n title: water production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000453\n multivalued: false\n alias: water_prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n water_temp_regm:\n name: water_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple regimens\n title: water temperature regimen\n examples:\n - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000590\n multivalued: true\n alias: water_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n watering_regm:\n name: watering_regm\n description: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple regimens\n title: watering regimen\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000591\n multivalued: true\n alias: watering_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n weekday:\n name: weekday\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The day of the week when sampling occurred\n title: weekday\n examples:\n - value: Sunday\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weekday\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000848\n multivalued: false\n alias: weekday\n owner: Biosample\n domain_of:\n - Biosample\n range: weekday_enum\n win:\n name: win\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n title: well identification number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - well identification number\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000297\n multivalued: false\n alias: win\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wind_direction:\n name: wind_direction\n annotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\n description: Wind direction is the direction from which a wind originates\n title: wind direction\n examples:\n - value: Northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind direction\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000757\n multivalued: false\n alias: wind_direction\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n wind_speed:\n name: wind_speed\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Speed of wind measured at the time of sampling\n title: wind speed\n examples:\n - value: 21 kilometer per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind speed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000118\n multivalued: false\n alias: wind_speed\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n window_cond:\n name: window_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the window at the time of sampling\n title: window condition\n examples:\n - value: rupture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000849\n multivalued: false\n alias: window_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cond_enum\n window_cover:\n name: window_cover\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of window covering\n title: window covering\n examples:\n - value: curtains\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window covering\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000850\n multivalued: false\n alias: window_cover\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cover_enum\n window_horiz_pos:\n name: window_horiz_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal position of the window on the wall\n title: window horizontal position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window horizontal position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000851\n multivalued: false\n alias: window_horiz_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_horiz_pos_enum\n window_loc:\n name: window_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the window within the room\n title: window location\n examples:\n - value: west\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000852\n multivalued: false\n alias: window_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: window_loc_enum\n window_mat:\n name: window_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a window\n title: window material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000853\n multivalued: false\n alias: window_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: window_mat_enum\n window_open_freq:\n name: window_open_freq\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times windows are opened per week\n title: window open frequency\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window open frequency\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000246\n multivalued: false\n alias: window_open_freq\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_size:\n name: window_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The window's length and width\n title: window area/size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window area/size\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit} x {float} {unit}'\n slot_uri: MIXS:0000224\n multivalued: false\n alias: window_size\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_status:\n name: window_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Defines whether the windows were open or closed during environmental\n testing\n title: window status\n examples:\n - value: open\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window status\n rank: 1000\n is_a: core field\n string_serialization: '[closed|open]'\n slot_uri: MIXS:0000855\n multivalued: false\n alias: window_status\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n window_type:\n name: window_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of windows\n title: window type\n examples:\n - value: fixed window\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000856\n multivalued: false\n alias: window_type\n owner: Biosample\n domain_of:\n - Biosample\n range: window_type_enum\n window_vert_pos:\n name: window_vert_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The vertical position of the window on the wall\n title: window vertical position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window vertical position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000857\n multivalued: false\n alias: window_vert_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_vert_pos_enum\n window_water_mold:\n name: window_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the window.\n title: window signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000854\n multivalued: false\n alias: window_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n xylene:\n name: xylene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of xylene in the sample\n title: xylene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - xylene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000156\n multivalued: false\n alias: xylene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n zinc:\n name: zinc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of zinc in the sample\n title: zinc\n examples:\n - value: 2.5 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - zinc\n rank: 1000\n is_a: attribute\n alias: zinc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n community:\n name: community\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: community\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n host_name:\n name: host_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: host_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n location:\n name: location\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: location\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: Biosample\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n ncbi_taxonomy_name:\n name: ncbi_taxonomy_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_taxonomy_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n proport_woa_temperature:\n name: proport_woa_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: proport_woa_temperature\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n salinity_category:\n name: salinity_category\n description: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\n notes:\n - maps to gold:salinity\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-metadata/pull/297\n rank: 1000\n alias: salinity_category\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sample_collection_site:\n name: sample_collection_site\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_collection_site\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soluble_iron_micromol:\n name: soluble_iron_micromol\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: soluble_iron_micromol\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n subsurface_depth:\n name: subsurface_depth\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subsurface_depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_absorb2:\n name: dna_absorb2\n description: 260/230 measurement of DNA sample purity\n title: DNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_collect_site:\n name: dna_collect_site\n description: Provide information on the site your DNA sample was collected from\n title: DNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: dna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: dna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n dna_cont_type:\n name: dna_cont_type\n description: Tube or plate (96-well)\n title: DNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: dna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: JgiContTypeEnum\n recommended: true\n dna_container_id:\n name: dna_container_id\n title: DNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: dna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_dnase:\n name: dna_dnase\n title: DNase treatment DNA\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dna_dnase\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: YesNoEnum\n recommended: true\n dna_isolate_meth:\n name: dna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: DNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{text}'\n alias: dna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_organisms:\n name: dna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: DNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: dna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_project_contact:\n name: dna_project_contact\n title: DNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: dna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_samp_id:\n name: dna_samp_id\n title: DNA sample ID\n todos:\n - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will\n be prefilled?\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: dna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_sample_format:\n name: dna_sample_format\n description: Solution in which the DNA sample has been suspended\n title: DNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: dna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: dna_sample_format_enum\n recommended: true\n dna_sample_name:\n name: dna_sample_name\n description: Give the DNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: DNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: dna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project:\n name: dna_seq_project\n title: DNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: dna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_pi:\n name: dna_seq_project_pi\n title: DNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: dna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_name:\n name: dna_seq_project_name\n title: DNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metagenomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: dna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_volume:\n name: dna_volume\n title: DNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: dna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n proposal_dna:\n name: proposal_dna\n title: DNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_dna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dnase_rna:\n name: dnase_rna\n title: DNase treated\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dnase_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: YesNoEnum\n recommended: true\n proposal_rna:\n name: proposal_rna\n title: RNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_absorb1:\n name: rna_absorb1\n description: 260/280 measurement of RNA sample purity\n title: RNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: rna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_absorb2:\n name: rna_absorb2\n description: 260/230 measurement of RNA sample purity\n title: RNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: rna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_collect_site:\n name: rna_collect_site\n description: Provide information on the site your RNA sample was collected from\n title: RNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: rna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_concentration:\n name: rna_concentration\n title: RNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: rna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n rna_cont_type:\n name: rna_cont_type\n description: Tube or plate (96-well)\n title: RNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: rna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: JgiContTypeEnum\n recommended: true\n rna_cont_well:\n name: rna_cont_well\n title: RNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: rna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n rna_container_id:\n name: rna_container_id\n title: RNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: rna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_isolate_meth:\n name: rna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: RNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{text}'\n alias: rna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_organisms:\n name: rna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: RNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: rna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_project_contact:\n name: rna_project_contact\n title: RNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: rna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_samp_id:\n name: rna_samp_id\n title: RNA sample ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: rna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_sample_format:\n name: rna_sample_format\n description: Solution in which the RNA sample has been suspended\n title: RNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: rna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: rna_sample_format_enum\n recommended: true\n rna_sample_name:\n name: rna_sample_name\n description: Give the RNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: RNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: rna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n rna_seq_project:\n name: rna_seq_project\n title: RNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: rna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_pi:\n name: rna_seq_project_pi\n title: RNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: rna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_name:\n name: rna_seq_project_name\n title: RNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metatranscriptomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: rna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_volume:\n name: rna_volume\n title: RNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: rna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n collection_date_inc:\n name: collection_date_inc\n description: Date the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{date, arbitrary precision}'\n alias: collection_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time:\n name: collection_time\n description: The time of sampling, either as an instance (single point) or interval.\n title: collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{time, seconds optional}'\n alias: collection_time\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time_inc:\n name: collection_time_inc\n description: Time the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{time, seconds optional}'\n alias: collection_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n experimental_factor_other:\n name: experimental_factor_other\n description: Other details about your sample that you feel can't be accurately\n represented in the available columns.\n title: experimental factor- other\n comments:\n - This slot accepts open-ended text about your sample.\n - We recommend using key:value pairs.\n - Provided pairs will be considered for inclusion as future slots/terms in this\n data collection template.\n examples:\n - value: 'experimental treatment: value'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n string_serialization: '{text}'\n alias: experimental_factor_other\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n filter_method:\n name: filter_method\n description: Type of filter used or how the sample was filtered\n title: filter method\n comments:\n - describe the filter or provide a catalog number and manufacturer\n examples:\n - value: C18\n - value: Basix PES, 13-100-106 FisherSci\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{text}'\n alias: filter_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n isotope_exposure:\n name: isotope_exposure\n description: List isotope exposure or addition applied to your sample.\n title: isotope exposure/addition\n todos:\n - Can we make the H218O correctly super and subscripted?\n comments:\n - This is required when your experimental design includes the use of isotopically\n labeled compounds\n examples:\n - value: 13C glucose\n - value: H218O\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 16\n string_serialization: '{termLabel} {[termID]}; {timestamp}'\n alias: isotope_exposure\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_c_meth:\n name: micro_biomass_c_meth\n description: Reference or method used in determining microbial biomass carbon\n title: microbial biomass carbon method\n todos:\n - How should we separate values? | or ;? lets be consistent\n comments:\n - required if \"microbial_biomass_c\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_n_meth:\n name: micro_biomass_n_meth\n description: Reference or method used in determining microbial biomass nitrogen\n title: microbial biomass nitrogen method\n comments:\n - required if \"microbial_biomass_n\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_n_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_c:\n name: microbial_biomass_c\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass carbon\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug C/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_c\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_n:\n name: microbial_biomass_n\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass nitrogen\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug N/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_n\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass:\n name: non_microb_biomass\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g.insect, plant, total. Can include multiple measurements separated\n by ;\n title: non-microbial biomass\n examples:\n - value: insect 0.23 ug; plant 1g\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n string_serialization: '{text};{float} {unit}'\n alias: non_microb_biomass\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass_method:\n name: non_microb_biomass_method\n description: Reference or method used in determining biomass\n title: non-microbial biomass method\n comments:\n - required if \"non-microbial biomass\" is provided\n examples:\n - value: https://doi.org/10.1038/s41467-021-26181-3\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: non_microb_biomass_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n org_nitro_method:\n name: org_nitro_method\n description: Method used for obtaining organic nitrogen\n title: organic nitrogen method\n comments:\n - required if \"org_nitro\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(85)90144-0\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: org_nitro_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n other_treatment:\n name: other_treatment\n description: Other treatments applied to your samples that are not applicable\n to the provided fields\n title: other treatments\n comments:\n - This is an open text field to provide any treatments that cannot be captured\n in the provided slots.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: other_treatment\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_date_inc:\n name: start_date_inc\n description: Date the incubation was started. Only relevant for incubation samples.\n title: incubation start date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: 2021-04-15, 2021-04 and 2021 are all acceptable.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{date, arbitrary precision}'\n alias: start_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_time_inc:\n name: start_time_inc\n description: Time the incubation was started. Only relevant for incubation samples.\n title: incubation start time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: 13:33 or 13:33:55\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{time, seconds optional}'\n alias: start_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n project_id:\n name: project_id\n description: Proposal IDs or names associated with dataset\n title: project ID\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: project_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n replicate_number:\n name: replicate_number\n description: If sending biological replicates, indicate the rep number here.\n title: replicate number\n comments:\n - This will guide staff in ensuring your samples are blocked & randomized correctly\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{integer}'\n alias: replicate_number\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_shipped:\n name: sample_shipped\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample sent to EMSL.\n title: sample shipped amount\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: 15 g\n - value: 100 uL\n - value: 5 mL\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{float} {unit}'\n alias: sample_shipped\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_type:\n name: sample_type\n description: Type of sample being submitted\n title: sample type\n comments:\n - This can vary from 'environmental package' if the sample is an extraction.\n examples:\n - value: water extracted soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n alias: sample_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: sample_type_enum\n recommended: true\n technical_reps:\n name: technical_reps\n description: If sending technical replicates of the same sample, indicate the\n replicate count.\n title: number technical replicate\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{integer}'\n alias: technical_reps\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n analysis_type:\n name: analysis_type\n description: Select all the data types associated or available for this biosample\n title: analysis/data type\n examples:\n - value: metagenomics; metabolomics; proteomics\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIxS:investigation_type\n rank: 3\n multivalued: true\n alias: analysis_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: analysis_type_enum\n recommended: true\n sample_link:\n name: sample_link\n description: A unique identifier to assign parent-child, subsample, or sibling\n samples. This is relevant when a sample or other material was used to generate\n the new sample.\n title: sample linkage\n comments:\n - 'This field allows multiple entries separated by ; (Examples: Soil collected\n from the field will link with the soil used in an incubation. The soil a plant\n was grown in links to the plant sample. An original culture sample was transferred\n to a new vial and generated a new sample)'\n examples:\n - value: IGSN:DSJ0284\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{text}:{text}'\n multivalued: true\n alias: sample_link\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: string\n recommended: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Biosample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Biosample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\n notes:\n - 'id is already required to be unique because it is the identifier in Biosample''s\n parent class, NamedThing. Remember, notes like this could be exposed to end\n users. CJM suggested YAML # comment'\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nFunding-based, sample location-based, or experimental method-based defined categories
URI: BiosampleCategoryEnum
"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":"name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n LTER:\n text: LTER\n meaning: https://lternet.edu/\n title: National Science Foundation's Long Term Ecological Research Network\n SIP:\n text: SIP\n SFA:\n text: SFA\n description: Science Focus Area projects funded through the Department of Energy\n Office of Science Biological and Environmental Research Program\n meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n title: Department of Energy Office of Science Biological and Environmental Research\n Program Laboratory Science Focus Areas\n FICUS:\n text: FICUS\n meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n title: Facilities Integrating Collaborations for User Science\n NEON:\n text: NEON\n meaning: https://www.neonscience.org\n title: National Science Foundation's National Ecological Observatory Network\n\nA process that takes one or more biosamples as inputs and generates one or more biosamples as outputs. An example of an output includes samples cultivated from another sample.
URI: nmdc:BiosampleProcessing
classDiagram\n class BiosampleProcessing\n PlannedProcess <|-- BiosampleProcessing\n\n\n BiosampleProcessing <|-- Pooling\n BiosampleProcessing <|-- Extraction\n BiosampleProcessing <|-- LibraryPreparation\n\n\n BiosampleProcessing : alternative_identifiers\n\n BiosampleProcessing : description\n\n BiosampleProcessing : end_date\n\n BiosampleProcessing : has_input\n\n BiosampleProcessing --|> Biosample : has_input\n\n BiosampleProcessing : has_output\n\n BiosampleProcessing --|> NamedThing : has_output\n\n BiosampleProcessing : id\n\n BiosampleProcessing : name\n\n BiosampleProcessing : protocol_link\n\n BiosampleProcessing --|> Protocol : protocol_link\n\n BiosampleProcessing : start_date\n\n\nname: BiosampleProcessing\ndescription: A process that takes one or more biosamples as inputs and generates one\n or more biosamples as outputs. An example of an output includes samples cultivated\n from another sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- material processing\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nslots:\n- has_input\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n\nname: BiosampleProcessing\ndescription: A process that takes one or more biosamples as inputs and generates one\n or more biosamples as outputs. An example of an output includes samples cultivated\n from another sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- material processing\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: BiosampleProcessing\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: BiosampleProcessing\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: BiosampleProcessing\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: BiosampleProcessing\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: BiosampleProcessing\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: BiosampleProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsmprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: BiosampleProcessing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: BiosampleProcessing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: BiosampleProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: BioticRelationshipEnum
"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":"name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n free living:\n text: free living\n parasite:\n text: parasite\n commensal:\n text: commensal\n symbiont:\n text: symbiont\n\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
A value that is a boolean
URI: nmdc:BooleanValue
classDiagram\n class BooleanValue\n AttributeValue <|-- BooleanValue\n\n BooleanValue : has_boolean_value\n\n BooleanValue : has_raw_value\n\n BooleanValue : was_generated_by\n\n BooleanValue --|> Activity : was_generated_by\n\n\nname: BooleanValue\ndescription: A value that is a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_boolean_value\n\nname: BooleanValue\ndescription: A value that is a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_boolean_value:\n name: has_boolean_value\n description: Links a quantity value to a boolean\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: false\n alias: has_boolean_value\n owner: BooleanValue\n domain_of:\n - BooleanValue\n range: boolean\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: BooleanValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: BooleanValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: BuildDocsEnum
"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":"name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building information model:\n text: building information model\n commissioning report:\n text: commissioning report\n complaint logs:\n text: complaint logs\n contract administration:\n text: contract administration\n cost estimate:\n text: cost estimate\n janitorial schedules or logs:\n text: janitorial schedules or logs\n maintenance plans:\n text: maintenance plans\n schedule:\n text: schedule\n sections:\n text: sections\n shop drawings:\n text: shop drawings\n submittals:\n text: submittals\n ventilation system:\n text: ventilation system\n windows:\n text: windows\n\nURI: BuildOccupTypeEnum
"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":"name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n office:\n text: office\n market:\n text: market\n restaurant:\n text: restaurant\n residence:\n text: residence\n school:\n text: school\n residential:\n text: residential\n commercial:\n text: commercial\n low rise:\n text: low rise\n high rise:\n text: high rise\n wood framed:\n text: wood framed\n health care:\n text: health care\n airport:\n text: airport\n sports complex:\n text: sports complex\n\nURI: BuildingSettingEnum
"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":"name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n urban:\n text: urban\n suburban:\n text: suburban\n exurban:\n text: exurban\n rural:\n text: rural\n\nAn integer value that corresponds to a size in bytes
URI: xsd:long
base: int
uri: xsd:long
URI: CeilCondEnum
"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":"name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: CeilFinishMatEnum
"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":"name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drywall:\n text: drywall\n mineral fibre:\n text: mineral fibre\n tiles:\n text: tiles\n PVC:\n text: PVC\n plasterboard:\n text: plasterboard\n metal:\n text: metal\n fiberglass:\n text: fiberglass\n stucco:\n text: stucco\n mineral wool/calcium silicate:\n text: mineral wool/calcium silicate\n wood:\n text: wood\n\nURI: CeilTextureEnum
"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":"name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: CeilTypeEnum
"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":"name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cathedral:\n text: cathedral\n dropped:\n text: dropped\n concave:\n text: concave\n barrel-shaped:\n text: barrel-shaped\n coffered:\n text: coffered\n cove:\n text: cove\n stretched:\n text: stretched\n\nA MIxS checklist. These can be combined with packages
URI: Checklist
"},{"location":"Checklist/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Checklist/#schema-source","title":"Schema Source","text":"A combination of a checklist and a package
URI: ChecklistPackageCombination
"},{"location":"ChecklistPackageCombination/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChecklistPackageCombination/#schema-source","title":"Schema Source","text":"An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states
URI: nmdc:ChemicalEntity
classDiagram\n class ChemicalEntity\n OntologyClass <|-- ChemicalEntity\n\n ChemicalEntity : alternative_identifiers\n\n ChemicalEntity : chemical_formula\n\n ChemicalEntity : description\n\n ChemicalEntity : id\n\n ChemicalEntity : inchi\n\n ChemicalEntity : inchi_key\n\n ChemicalEntity : name\n\n ChemicalEntity : smiles\n\n\nInstances of this class should have identifiers with one of the following prefixes:
cas
CHEBI
CHEMBL.COMPOUND
DRUGBANK
HMDB
KEGG.COMPOUND
MESH
PUBCHEM.COMPOUND
name: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- chemical_formula\n- inchi\n- inchi_key\n- smiles\n\nname: ChemicalEntity\nid_prefixes:\n- cas\n- CHEBI\n- CHEMBL.COMPOUND\n- DRUGBANK\n- HMDB\n- KEGG.COMPOUND\n- MESH\n- PUBCHEM.COMPOUND\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n chemical_formula:\n name: chemical_formula\n description: A generic grouping for molecular formulae and empirical formulae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_formula\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n inchi:\n name: inchi\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: inchi\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n inchi_key:\n name: inchi_key\n notes:\n - 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: inchi_key\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n smiles:\n name: smiles\n description: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: smiles\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalEntity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalEntity\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: ChemicalEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:CollectingBiosamplesFromSite
classDiagram\n class CollectingBiosamplesFromSite\n PlannedProcess <|-- CollectingBiosamplesFromSite\n\n CollectingBiosamplesFromSite : alternative_identifiers\n\n CollectingBiosamplesFromSite : description\n\n CollectingBiosamplesFromSite : end_date\n\n CollectingBiosamplesFromSite : has_input\n\n CollectingBiosamplesFromSite --|> Site : has_input\n\n CollectingBiosamplesFromSite : has_output\n\n CollectingBiosamplesFromSite --|> Biosample : has_output\n\n CollectingBiosamplesFromSite : id\n\n CollectingBiosamplesFromSite : name\n\n CollectingBiosamplesFromSite : protocol_link\n\n CollectingBiosamplesFromSite --|> Protocol : protocol_link\n\n CollectingBiosamplesFromSite : start_date\n\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: CollectingBiosamplesFromSite\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Site\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: CollectingBiosamplesFromSite\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: CollectingBiosamplesFromSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ContainerTypeEnum
"},{"location":"ContainerTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description screw_top_conical None"},{"location":"ContainerTypeEnum/#slots","title":"Slots","text":"Name Description container_type"},{"location":"ContainerTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerTypeEnum/#schema-source","title":"Schema Source","text":"name: ContainerTypeEnum\ntitle: Container type enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n screw_top_conical:\n text: screw_top_conical\n title: Screw top conical tube\n aliases:\n - falcon tube\n\nA controlled term or class from an ontology, requiring the presence of term with an id
URI: nmdc:ControlledIdentifiedTermValue
classDiagram\n class ControlledIdentifiedTermValue\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n\n ControlledIdentifiedTermValue : has_raw_value\n\n ControlledIdentifiedTermValue : term\n\n ControlledIdentifiedTermValue --|> OntologyClass : term\n\n ControlledIdentifiedTermValue : was_generated_by\n\n ControlledIdentifiedTermValue --|> Activity : was_generated_by\n\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n domain_of:\n - ControlledTermValue\n required: true\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n domain_of:\n - ControlledTermValue\n required: true\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: ControlledTermValue\n alias: term\n owner: ControlledIdentifiedTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n required: true\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ControlledIdentifiedTermValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ControlledIdentifiedTermValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nA controlled term or class from an ontology
URI: nmdc:ControlledTermValue
classDiagram\n class ControlledTermValue\n AttributeValue <|-- ControlledTermValue\n\n\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n\n\n ControlledTermValue : has_raw_value\n\n ControlledTermValue : term\n\n ControlledTermValue --|> OntologyClass : term\n\n ControlledTermValue : was_generated_by\n\n ControlledTermValue --|> Activity : was_generated_by\n\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: ControlledTermValue\n alias: term\n owner: ControlledTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ControlledTermValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ControlledTermValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nThis class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/) and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0
URI: prov:Association
classDiagram\n class CreditAssociation\n CreditAssociation : applied_role\n\n CreditAssociation --|> credit enum : applied_role\n\n CreditAssociation : applied_roles\n\n CreditAssociation --|> credit enum : applied_roles\n\n CreditAssociation : applies_to_person\n\n CreditAssociation --|> PersonValue : applies_to_person\n\n CreditAssociation : type\n\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/)\n and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_role\n- applied_roles\n- type\nclass_uri: prov:Association\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role (https://casrai.org/credit/)\n and for a person value Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n applies_to_person:\n name: applies_to_person\n todos:\n - prov:agent takes an Agent object. Is a person value an Agent? Also try to relate\n to principal investigator slot? could include OBI:0000103 principal investigator\n role... do we need to define the OBI prefix?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n alias: applies_to_person\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: PersonValue\n required: true\n applied_role:\n name: applied_role\n deprecated: A credit association may have multiple roles. So, use the applied\n roles slot.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n slot_uri: prov:hadRole\n alias: applied_role\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: credit enum\n applied_roles:\n name: applied_roles\n annotations:\n display_hint:\n tag: display_hint\n value: 'Identify all CRediT roles associated with this contributor. CRediT\n Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n https://credit.niso.org/'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: CreditAssociation\n multivalued: true\n alias: applied_roles\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: credit enum\n required: true\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: CreditAssociation\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\nclass_uri: prov:Association\n\nURI: CreditEnum
"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_role applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":"name: credit enum\ncomments:\n- credit enums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Conceptualization:\n text: Conceptualization\n description: Conceptualization\n Data curation:\n text: Data curation\n description: Data curation\n Formal Analysis:\n text: Formal Analysis\n description: Formal Analysis\n Funding acquisition:\n text: Funding acquisition\n description: Funding acquisition\n Investigation:\n text: Investigation\n description: Investigation\n Methodology:\n text: Methodology\n description: Methodology\n Project administration:\n text: Project administration\n description: Project administration\n Resources:\n text: Resources\n description: Resources\n Software:\n text: Software\n description: Software\n Supervision:\n text: Supervision\n description: Supervision\n Validation:\n text: Validation\n description: Validation\n Visualization:\n text: Visualization\n description: Visualization\n Writing original draft:\n text: Writing original draft\n description: Writing \u2013 original draft\n Writing review and editing:\n text: Writing review and editing\n description: Writing \u2013 review & editing\n Principal Investigator:\n text: Principal Investigator\n description: principal investigator role\n meaning: OBI:0000103\n Submitter:\n text: Submitter\n description: the person(s) who enter study and biosample metadata into the NMDC\n submission portal\n meaning: EFO:0001741\n\nURI: CurLandUseEnum
"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":"name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n badlands:\n text: badlands\n cities:\n text: cities\n conifers:\n text: conifers\n annotations:\n originally:\n tag: originally\n value: conifers (e.g. pine,spruce,fir,cypress)\n examples:\n - value: cypress\n - value: fir\n - value: pine\n - value: spruce\n crop trees:\n text: crop trees\n annotations:\n originally:\n tag: originally\n value: crop trees (nuts,fruit,christmas trees,nursery trees)\n examples:\n - value: christmas trees\n - value: fruit\n - value: nursery trees\n - value: nuts\n farmstead:\n text: farmstead\n gravel:\n text: gravel\n hardwoods:\n text: hardwoods\n annotations:\n originally:\n tag: originally\n value: hardwoods (e.g. oak,hickory,elm,aspen)\n examples:\n - value: aspen\n - value: elm\n - value: hickory\n - value: oak\n hayland:\n text: hayland\n horticultural plants:\n text: horticultural plants\n annotations:\n originally:\n tag: originally\n value: horticultural plants (e.g. tulips)\n examples:\n - value: tulips\n industrial areas:\n text: industrial areas\n intermixed hardwood and conifers:\n text: intermixed hardwood and conifers\n marshlands:\n text: marshlands\n annotations:\n originally:\n tag: originally\n value: marshlands (grass,sedges,rushes)\n examples:\n - value: grass\n - value: rushes\n - value: sedgees\n meadows:\n text: meadows\n annotations:\n originally:\n tag: originally\n value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n examples:\n - value: alfalfa\n - value: bromegrass\n - value: fescue\n - value: grasses\n - value: timothy\n mines/quarries:\n text: mines/quarries\n mudflats:\n text: mudflats\n oil waste areas:\n text: oil waste areas\n pastureland:\n text: pastureland\n annotations:\n originally:\n tag: originally\n value: pastureland (grasslands used for livestock grazing)\n comments:\n - grasslands used for livestock grazing\n permanent snow or ice:\n text: permanent snow or ice\n rainforest:\n text: rainforest\n annotations:\n originally:\n tag: originally\n value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n comments:\n - evergreen forest receiving greater than 406 cm annual rainfall\n rangeland:\n text: rangeland\n roads/railroads:\n text: roads/railroads\n rock:\n text: rock\n row crops:\n text: row crops\n saline seeps:\n text: saline seeps\n salt flats:\n text: salt flats\n sand:\n text: sand\n shrub crops:\n text: shrub crops\n annotations:\n originally:\n tag: originally\n value: shrub crops (blueberries,nursery ornamentals,filberts)\n examples:\n - value: blueberries\n - value: filberts\n - value: nursery ornamentals\n shrub land:\n text: shrub land\n annotations:\n originally:\n tag: originally\n value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n examples:\n - value: creosote bush\n - value: eucalyptus\n - value: mesquite\n - value: sage-brush\n - value: shrub oak\n small grains:\n text: small grains\n successional shrub land:\n text: successional shrub land\n annotations:\n originally:\n tag: originally\n value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n dogwoods,blackberries)\n examples:\n - value: blackberries\n - value: chokecherry\n - value: hazels\n - value: shrub dogwoods\n - value: sumacs\n - value: tree saplings\n swamp:\n text: swamp\n annotations:\n originally:\n tag: originally\n value: swamp (permanent or semi-permanent water body dominated by woody plants)\n comments:\n - permanent or semi-permanent water body dominated by woody plants\n tropical:\n text: tropical\n annotations:\n originally:\n tag: originally\n value: tropical (e.g. mangrove,palms)\n examples:\n - value: mangrove\n - value: palms\n tundra:\n text: tundra\n annotations:\n originally:\n tag: originally\n value: tundra (mosses,lichens)\n examples:\n - value: lichens\n - value: mosses\n vegetable crops:\n text: vegetable crops\n vine crops:\n text: vine crops\n annotations:\n originally:\n tag: originally\n value: vine crops (grapes)\n examples:\n - value: grapes\n\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
URI: nmdc:DataObject
classDiagram\n class DataObject\n NamedThing <|-- DataObject\n\n DataObject : alternative_identifiers\n\n DataObject : compression_type\n\n DataObject : data_object_type\n\n DataObject --|> file type enum : data_object_type\n\n DataObject : description\n\n DataObject : file_size_bytes\n\n DataObject : id\n\n DataObject : md5_checksum\n\n DataObject : name\n\n DataObject : type\n\n DataObject : url\n\n DataObject : was_generated_by\n\n DataObject --|> Activity : was_generated_by\n\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\ncomments:\n- removed id_prefixes value of GOLD, since we are now using pattern-based id validation\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslots:\n- file_size_bytes\n- md5_checksum\n- data_object_type\n- compression_type\n- was_generated_by\n- url\n- type\nslot_usage:\n name:\n name: name\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n required: true\n description:\n name: description\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nnotes:\n- removed previous id_prefixes value of GOLD, since we are now using pattern-based\n id validation\ncomments:\n- removed id_prefixes value of GOLD, since we are now using pattern-based id validation\nin_subset:\n- data object subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n name:\n name: name\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n required: true\n description:\n name: description\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n file_size_bytes:\n name: file_size_bytes\n description: Size of the file in bytes\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: file_size_bytes\n owner: DataObject\n domain_of:\n - DataObject\n range: bytes\n md5_checksum:\n name: md5_checksum\n description: MD5 checksum of file (pre-compressed)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: md5_checksum\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n data_object_type:\n name: data_object_type\n description: The type of file represented by the data object.\n examples:\n - value: FT ICR-MS Analysis Results\n - value: GC-MS Metabolomics Results\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: data_object_type\n owner: DataObject\n domain_of:\n - DataObject\n range: file type enum\n compression_type:\n name: compression_type\n description: If provided, specifies the compression type\n todos:\n - consider enum\n examples:\n - value: gzip\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: compression_type\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: DataObject\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: DataObject\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: DataObject\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: DataObject\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataObject\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataObject\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: DataObject\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSubset consisting of the data objects that either inputs or outputs of processes or workflows.
URI: DataObjectSubset
"},{"location":"DataObjectSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataObjectSubset/#schema-source","title":"Schema Source","text":"An object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
"},{"location":"Database/","title":"Class: Database","text":"An abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest
URI: nmdc:Database
classDiagram\n class Database\n Database : activity_set\n\n Database --|> WorkflowExecutionActivity : activity_set\n\n Database : biosample_set\n\n Database --|> Biosample : biosample_set\n\n Database : collecting_biosamples_from_site_set\n\n Database --|> CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n\n Database : data_object_set\n\n Database --|> DataObject : data_object_set\n\n Database : date_created\n\n Database : dissolving_activity_set\n\n Database --|> DissolvingActivity : dissolving_activity_set\n\n Database : etl_software_version\n\n Database : extraction_set\n\n Database --|> Extraction : extraction_set\n\n Database : field_research_site_set\n\n Database --|> FieldResearchSite : field_research_site_set\n\n Database : functional_annotation_agg\n\n Database --|> FunctionalAnnotationAggMember : functional_annotation_agg\n\n Database : functional_annotation_set\n\n Database --|> FunctionalAnnotation : functional_annotation_set\n\n Database : genome_feature_set\n\n Database --|> GenomeFeature : genome_feature_set\n\n Database : library_preparation_set\n\n Database --|> LibraryPreparation : library_preparation_set\n\n Database : mags_activity_set\n\n Database --|> MagsAnalysisActivity : mags_activity_set\n\n Database : material_sample_set\n\n Database --|> MaterialSample : material_sample_set\n\n Database : material_sampling_activity_set\n\n Database --|> MaterialSamplingActivity : material_sampling_activity_set\n\n Database : metabolomics_analysis_activity_set\n\n Database --|> MetabolomicsAnalysisActivity : metabolomics_analysis_activity_set\n\n Database : metagenome_annotation_activity_set\n\n Database --|> MetagenomeAnnotationActivity : metagenome_annotation_activity_set\n\n Database : metagenome_assembly_set\n\n Database --|> MetagenomeAssembly : metagenome_assembly_set\n\n Database : metagenome_sequencing_activity_set\n\n Database --|> MetagenomeSequencingActivity : metagenome_sequencing_activity_set\n\n Database : metaproteomics_analysis_activity_set\n\n Database --|> MetaproteomicsAnalysisActivity : metaproteomics_analysis_activity_set\n\n Database : metatranscriptome_activity_set\n\n Database --|> MetatranscriptomeActivity : metatranscriptome_activity_set\n\n Database : nom_analysis_activity_set\n\n Database --|> NomAnalysisActivity : nom_analysis_activity_set\n\n Database : omics_processing_set\n\n Database --|> OmicsProcessing : omics_processing_set\n\n Database : pooling_set\n\n Database --|> Pooling : pooling_set\n\n Database : processed_sample_set\n\n Database --|> ProcessedSample : processed_sample_set\n\n Database : reaction_activity_set\n\n Database --|> ReactionActivity : reaction_activity_set\n\n Database : read_based_taxonomy_analysis_activity_set\n\n Database --|> ReadBasedTaxonomyAnalysisActivity : read_based_taxonomy_analysis_activity_set\n\n Database : read_qc_analysis_activity_set\n\n Database --|> ReadQcAnalysisActivity : read_qc_analysis_activity_set\n\n Database : study_set\n\n Database --|> Study : study_set\n\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- functional_annotation_agg\n- library_preparation_set\n- processed_sample_set\n- extraction_set\n- activity_set\n- biosample_set\n- data_object_set\n- dissolving_activity_set\n- functional_annotation_set\n- genome_feature_set\n- mags_activity_set\n- material_sample_set\n- material_sampling_activity_set\n- metabolomics_analysis_activity_set\n- metagenome_annotation_activity_set\n- metagenome_assembly_set\n- metagenome_sequencing_activity_set\n- metaproteomics_analysis_activity_set\n- metatranscriptome_activity_set\n- nom_analysis_activity_set\n- omics_processing_set\n- reaction_activity_set\n- read_qc_analysis_activity_set\n- read_based_taxonomy_analysis_activity_set\n- study_set\n- field_research_site_set\n- collecting_biosamples_from_site_set\n- date_created\n- etl_software_version\n- metatranscriptome_activity_set\n- pooling_set\n- extraction_set\nslot_usage:\n date_created:\n name: date_created\n todos:\n - description\n domain_of:\n - Database\n etl_software_version:\n name: etl_software_version\n todos:\n - description\n domain_of:\n - Database\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n todos:\n - description\n domain_of:\n - Database\ntree_root: true\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslot_usage:\n date_created:\n name: date_created\n todos:\n - description\n domain_of:\n - Database\n etl_software_version:\n name: etl_software_version\n todos:\n - description\n domain_of:\n - Database\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n todos:\n - description\n domain_of:\n - Database\nattributes:\n functional_annotation_agg:\n name: functional_annotation_agg\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: functional_annotation_agg\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotationAggMember\n inlined: true\n inlined_as_list: true\n library_preparation_set:\n name: library_preparation_set\n description: This property links a database object to the set of DNA extractions\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - library_construction_set\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: library_preparation_set\n owner: Database\n domain_of:\n - Database\n range: LibraryPreparation\n inlined_as_list: true\n processed_sample_set:\n name: processed_sample_set\n description: This property links a database object to the set of processed samples\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: processed_sample_set\n owner: Database\n domain_of:\n - Database\n range: ProcessedSample\n inlined_as_list: true\n extraction_set:\n name: extraction_set\n description: This property links a database object to the set of extractions within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: extraction_set\n owner: Database\n domain_of:\n - Database\n range: Extraction\n inlined_as_list: true\n activity_set:\n name: activity_set\n description: This property links a database object to the set of workflow activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: activity_set\n owner: Database\n domain_of:\n - Database\n range: WorkflowExecutionActivity\n inlined_as_list: true\n biosample_set:\n name: biosample_set\n description: This property links a database object to the set of samples within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: biosample_set\n owner: Database\n domain_of:\n - Database\n range: Biosample\n inlined_as_list: true\n data_object_set:\n name: data_object_set\n description: This property links a database object to the set of data objects\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: data_object_set\n owner: Database\n domain_of:\n - Database\n range: DataObject\n inlined_as_list: true\n dissolving_activity_set:\n name: dissolving_activity_set\n title: dissolving activity set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: dissolving_activity_set\n owner: Database\n domain_of:\n - Database\n range: DissolvingActivity\n inlined: true\n inlined_as_list: true\n functional_annotation_set:\n name: functional_annotation_set\n description: This property links a database object to the set of all functional\n annotations\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: functional_annotation_set\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotation\n inlined_as_list: true\n genome_feature_set:\n name: genome_feature_set\n description: This property links a database object to the set of all features\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: genome_feature_set\n owner: Database\n domain_of:\n - Database\n range: GenomeFeature\n inlined_as_list: true\n mags_activity_set:\n name: mags_activity_set\n description: This property links a database object to the set of MAGs analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: mags_activity_set\n owner: Database\n domain_of:\n - Database\n range: MagsAnalysisActivity\n inlined_as_list: true\n material_sample_set:\n name: material_sample_set\n title: material sample set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: material_sample_set\n owner: Database\n domain_of:\n - Database\n range: MaterialSample\n inlined: true\n inlined_as_list: true\n material_sampling_activity_set:\n name: material_sampling_activity_set\n title: material sampling activity set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: material_sampling_activity_set\n owner: Database\n domain_of:\n - Database\n range: MaterialSamplingActivity\n inlined: true\n inlined_as_list: true\n metabolomics_analysis_activity_set:\n name: metabolomics_analysis_activity_set\n description: This property links a database object to the set of metabolomics\n analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metabolomics_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetabolomicsAnalysisActivity\n inlined_as_list: true\n metagenome_annotation_activity_set:\n name: metagenome_annotation_activity_set\n description: This property links a database object to the set of metagenome annotation\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_annotation_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeAnnotationActivity\n inlined_as_list: true\n metagenome_assembly_set:\n name: metagenome_assembly_set\n description: This property links a database object to the set of metagenome assembly\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_assembly_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeAssembly\n inlined_as_list: true\n metagenome_sequencing_activity_set:\n name: metagenome_sequencing_activity_set\n description: This property links a database object to the set of metagenome sequencing\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metagenome_sequencing_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetagenomeSequencingActivity\n inlined_as_list: true\n metaproteomics_analysis_activity_set:\n name: metaproteomics_analysis_activity_set\n description: This property links a database object to the set of metaproteomics\n analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: metaproteomics_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetaproteomicsAnalysisActivity\n inlined_as_list: true\n metatranscriptome_activity_set:\n name: metatranscriptome_activity_set\n description: This property links a database object to the set of metatranscriptome\n analysis activities.\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: metatranscriptome_activity_set\n owner: Database\n domain_of:\n - Database\n range: MetatranscriptomeActivity\n inlined_as_list: true\n nom_analysis_activity_set:\n name: nom_analysis_activity_set\n description: This property links a database object to the set of natural organic\n matter (NOM) analysis activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: nom_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: NomAnalysisActivity\n inlined_as_list: true\n omics_processing_set:\n name: omics_processing_set\n description: This property links a database object to the set of omics processings\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: omics_processing_set\n owner: Database\n domain_of:\n - Database\n range: OmicsProcessing\n inlined_as_list: true\n reaction_activity_set:\n name: reaction_activity_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: reaction_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReactionActivity\n inlined: true\n inlined_as_list: true\n read_qc_analysis_activity_set:\n name: read_qc_analysis_activity_set\n description: This property links a database object to the set of read QC analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: read_qc_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReadQcAnalysisActivity\n inlined_as_list: true\n read_based_taxonomy_analysis_activity_set:\n name: read_based_taxonomy_analysis_activity_set\n description: This property links a database object to the set of read based analysis\n activities.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: read_based_taxonomy_analysis_activity_set\n owner: Database\n domain_of:\n - Database\n range: ReadBasedTaxonomyAnalysisActivity\n inlined_as_list: true\n study_set:\n name: study_set\n description: This property links a database object to the set of studies within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: study_set\n owner: Database\n domain_of:\n - Database\n range: Study\n inlined_as_list: true\n field_research_site_set:\n name: field_research_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: field_research_site_set\n owner: Database\n domain_of:\n - Database\n range: FieldResearchSite\n inlined: true\n inlined_as_list: true\n collecting_biosamples_from_site_set:\n name: collecting_biosamples_from_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Database\n multivalued: true\n alias: collecting_biosamples_from_site_set\n owner: Database\n domain_of:\n - Database\n range: CollectingBiosamplesFromSite\n inlined: true\n inlined_as_list: true\n date_created:\n name: date_created\n description: from database class\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: date_created\n owner: Database\n domain_of:\n - Database\n range: string\n etl_software_version:\n name: etl_software_version\n description: from database class\n todos:\n - description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: etl_software_version\n owner: Database\n domain_of:\n - Database\n range: string\n pooling_set:\n name: pooling_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n domain: Database\n multivalued: true\n alias: pooling_set\n owner: Database\n domain_of:\n - Database\n range: Pooling\n inlined_as_list: true\ntree_root: true\n\na date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
A decimal degree expresses latitude or longitude as decimal fractions.
URI: xsd:decimal
base: float
uri: xsd:decimal
URI: DeposEnvEnum
"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":"name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Continental - Alluvial:\n text: Continental - Alluvial\n Continental - Aeolian:\n text: Continental - Aeolian\n Continental - Fluvial:\n text: Continental - Fluvial\n Continental - Lacustrine:\n text: Continental - Lacustrine\n Transitional - Deltaic:\n text: Transitional - Deltaic\n Transitional - Tidal:\n text: Transitional - Tidal\n Transitional - Lagoonal:\n text: Transitional - Lagoonal\n Transitional - Beach:\n text: Transitional - Beach\n Transitional - Lake:\n text: Transitional - Lake\n Marine - Shallow:\n text: Marine - Shallow\n Marine - Deep:\n text: Marine - Deep\n Marine - Reef:\n text: Marine - Reef\n Other - Evaporite:\n text: Other - Evaporite\n Other - Glacial:\n text: Other - Glacial\n Other - Volcanic:\n text: Other - Volcanic\n other:\n text: other\n\nURI: DeviceTypeEnum
"},{"location":"DeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description orbital_shaker None thermomixer None"},{"location":"DeviceTypeEnum/#slots","title":"Slots","text":"Name Description device_type"},{"location":"DeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: DeviceTypeEnum\ntitle: Shaker type enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n orbital_shaker:\n text: orbital_shaker\n title: Orbital shaker\n thermomixer:\n text: thermomixer\n title: Thermomixer\n\nURI: CHMO:0002773
classDiagram\n class DissolvingActivity\n DissolvingActivity : dissolution_aided_by\n\n DissolvingActivity --|> LabDevice : dissolution_aided_by\n\n DissolvingActivity : dissolution_reagent\n\n DissolvingActivity --|> SolventEnum : dissolution_reagent\n\n DissolvingActivity : dissolution_volume\n\n DissolvingActivity --|> QuantityValue : dissolution_volume\n\n DissolvingActivity : dissolved_in\n\n DissolvingActivity --|> MaterialContainer : dissolved_in\n\n DissolvingActivity : material_input\n\n DissolvingActivity --|> MaterialSample : material_input\n\n DissolvingActivity : material_output\n\n DissolvingActivity --|> MaterialSample : material_output\n\n\nname: DissolvingActivity\ntitle: Dissolving activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolution-activity\nslots:\n- dissolution_aided_by\n- dissolution_reagent\n- dissolution_volume\n- dissolved_in\n- material_input\n- material_output\nslot_usage:\n material_input:\n name: material_input\n examples:\n - value: somextract:6\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:7\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nclass_uri: CHMO:0002773\n\nname: DissolvingActivity\ntitle: Dissolving activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolution-activity\nslot_usage:\n material_input:\n name: material_input\n examples:\n - value: somextract:6\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:7\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nattributes:\n dissolution_aided_by:\n name: dissolution_aided_by\n title: dissolution aided by\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker\n rank: 1000\n alias: dissolution_aided_by\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: LabDevice\n inlined: true\n dissolution_reagent:\n name: dissolution_reagent\n title: dissolution reagent\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solvent\n rank: 1000\n alias: dissolution_reagent\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: SolventEnum\n dissolution_volume:\n name: dissolution_volume\n title: dissolution volume\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volume\n rank: 1000\n alias: dissolution_volume\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: QuantityValue\n inlined: true\n dissolved_in:\n name: dissolved_in\n title: dissolved in\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - container\n rank: 1000\n alias: dissolved_in\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n range: MaterialContainer\n inlined: true\n material_input:\n name: material_input\n title: material input\n examples:\n - value: somextract:6\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_input\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n range: MaterialSample\n material_output:\n name: material_output\n title: material output\n examples:\n - value: somextract:7\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_output\n owner: DissolvingActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\nclass_uri: CHMO:0002773\n\nURI: DnaSampleFormatEnum
"},{"location":"DnaSampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DnaSampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DnaSampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DnaSampleFormatEnum/#schema-source","title":"Schema Source","text":"name: dna_sample_format_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: DoorCompTypeEnum
"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":"name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metal covered:\n text: metal covered\n revolving:\n text: revolving\n sliding:\n text: sliding\n telescopic:\n text: telescopic\n\nURI: DoorCondEnum
"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":"name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: DoorDirectEnum
"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":"name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n inward:\n text: inward\n outward:\n text: outward\n sideways:\n text: sideways\n\nURI: DoorLocEnum
"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":"name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: DoorMatEnum
"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":"name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aluminum:\n text: aluminum\n cellular PVC:\n text: cellular PVC\n engineered plastic:\n text: engineered plastic\n fiberboard:\n text: fiberboard\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n thermoplastic alloy:\n text: thermoplastic alloy\n vinyl:\n text: vinyl\n wood:\n text: wood\n wood/plastic composite:\n text: wood/plastic composite\n\nURI: DoorMoveEnum
"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":"name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n folding:\n text: folding\n revolving:\n text: revolving\n rolling shutter:\n text: rolling shutter\n sliding:\n text: sliding\n swinging:\n text: swinging\n\nURI: DoorTypeEnum
"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":"name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n composite:\n text: composite\n metal:\n text: metal\n wooden:\n text: wooden\n\nURI: DoorTypeMetalEnum
"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":"name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n corrugated steel:\n text: corrugated steel\n hollow:\n text: hollow\n rolling shutters:\n text: rolling shutters\n steel plate:\n text: steel plate\n\nURI: DoorTypeWoodEnum
"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":"name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bettened and ledged:\n text: bettened and ledged\n battened:\n text: battened\n ledged and braced:\n text: ledged and braced\n ledged and framed:\n text: ledged and framed\n ledged, braced and frame:\n text: ledged, braced and frame\n framed and paneled:\n text: framed and paneled\n glashed or sash:\n text: glashed or sash\n flush:\n text: flush\n louvered:\n text: louvered\n wire gauged:\n text: wire gauged\n\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
URI: DrainageClassEnum
"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":"name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n very poorly:\n text: very poorly\n poorly:\n text: poorly\n somewhat poorly:\n text: somewhat poorly\n moderately well:\n text: moderately well\n well:\n text: well\n excessively drained:\n text: excessively drained\n\nURI: DrawingsEnum
"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":"name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n building navigation map:\n text: building navigation map\n diagram:\n text: diagram\n sketch:\n text: sketch\n\nURI: Environment
"},{"location":"Environment/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Environment/#schema-source","title":"Schema Source","text":"URI: nmdc:EnvironmentalMaterialTerm
classDiagram\n class EnvironmentalMaterialTerm\n OntologyClass <|-- EnvironmentalMaterialTerm\n\n EnvironmentalMaterialTerm : alternative_identifiers\n\n EnvironmentalMaterialTerm : description\n\n EnvironmentalMaterialTerm : id\n\n EnvironmentalMaterialTerm : name\n\n\nname: EnvironmentalMaterialTerm\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\n\nname: EnvironmentalMaterialTerm\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: EnvironmentalMaterialTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ExtWallOrientEnum
"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nURI: ExtWindowOrientEnum
"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nA CURIE representing an external identifier
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
typeof: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
A material separation in which a desired component of an input material is separated from the remainder.
URI: nmdc:Extraction
classDiagram\n class Extraction\n BiosampleProcessing <|-- Extraction\n\n Extraction : alternative_identifiers\n\n Extraction : description\n\n Extraction : end_date\n\n Extraction : extraction_method\n\n Extraction : extraction_target\n\n Extraction --|> ExtractionTargetEnum : extraction_target\n\n Extraction : has_input\n\n Extraction --|> Biosample : has_input\n\n Extraction : has_output\n\n Extraction --|> NamedThing : has_output\n\n Extraction : id\n\n Extraction : input_mass\n\n Extraction --|> QuantityValue : input_mass\n\n Extraction : name\n\n Extraction : processing_institution\n\n Extraction --|> processing_institution_enum : processing_institution\n\n Extraction : protocol_link\n\n Extraction --|> Protocol : protocol_link\n\n Extraction : quality_control_report\n\n Extraction --|> QualityControlReport : quality_control_report\n\n Extraction : start_date\n\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: BiosampleProcessing\nslots:\n- extraction_method\n- extraction_target\n- processing_institution\n- protocol_link\n- quality_control_report\n- input_mass\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n extraction_method:\n name: extraction_method\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: extraction_method\n owner: Extraction\n domain_of:\n - Extraction\n range: string\n extraction_target:\n name: extraction_target\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: extraction_target\n owner: Extraction\n domain_of:\n - Extraction\n range: ExtractionTargetEnum\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Extraction\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Extraction\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n quality_control_report:\n name: quality_control_report\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: quality_control_report\n owner: Extraction\n domain_of:\n - Extraction\n range: QualityControlReport\n input_mass:\n name: input_mass\n description: Total mass of sample used in activity.\n title: sample mass used\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample mass\n - sample weight\n exact_mappings:\n - MS:1000004\n rank: 1000\n alias: input_mass\n owner: Extraction\n domain_of:\n - Extraction\n range: QuantityValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: Extraction\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: Extraction\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Extraction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Extraction\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Extraction\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Extraction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ExtractionTargetEnum
"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_target"},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":"name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n metabolite:\n text: metabolite\n protein:\n text: protein\n\nURI: FaoClassEnum
"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":"name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Acrisols:\n text: Acrisols\n Andosols:\n text: Andosols\n Arenosols:\n text: Arenosols\n Cambisols:\n text: Cambisols\n Chernozems:\n text: Chernozems\n Ferralsols:\n text: Ferralsols\n Fluvisols:\n text: Fluvisols\n Gleysols:\n text: Gleysols\n Greyzems:\n text: Greyzems\n Gypsisols:\n text: Gypsisols\n Histosols:\n text: Histosols\n Kastanozems:\n text: Kastanozems\n Lithosols:\n text: Lithosols\n Luvisols:\n text: Luvisols\n Nitosols:\n text: Nitosols\n Phaeozems:\n text: Phaeozems\n Planosols:\n text: Planosols\n Podzols:\n text: Podzols\n Podzoluvisols:\n text: Podzoluvisols\n Rankers:\n text: Rankers\n Regosols:\n text: Regosols\n Rendzinas:\n text: Rendzinas\n Solonchaks:\n text: Solonchaks\n Solonetz:\n text: Solonetz\n Vertisols:\n text: Vertisols\n Yermosols:\n text: Yermosols\n\nA site, outside of a laboratory, from which biosamples may be collected.
URI: nmdc:FieldResearchSite
classDiagram\n class FieldResearchSite\n Site <|-- FieldResearchSite\n\n FieldResearchSite : alternative_identifiers\n\n FieldResearchSite : cur_vegetation\n\n FieldResearchSite --|> TextValue : cur_vegetation\n\n FieldResearchSite : description\n\n FieldResearchSite : elev\n\n FieldResearchSite --|> QuantityValue : elev\n\n FieldResearchSite : geo_loc_name\n\n FieldResearchSite --|> TextValue : geo_loc_name\n\n FieldResearchSite : habitat\n\n FieldResearchSite : id\n\n FieldResearchSite : lat_lon\n\n FieldResearchSite --|> GeolocationValue : lat_lon\n\n FieldResearchSite : local_class\n\n FieldResearchSite --|> TextValue : local_class\n\n FieldResearchSite : name\n\n FieldResearchSite : part_of\n\n FieldResearchSite --|> NamedThing : part_of\n\n FieldResearchSite : soil_type\n\n FieldResearchSite --|> TextValue : soil_type\n\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n multivalued: false\n alias: cur_vegetation\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n multivalued: false\n alias: elev\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: QuantityValue\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n multivalued: false\n alias: geo_loc_name\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n multivalued: false\n alias: lat_lon\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n multivalued: false\n alias: local_class\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n multivalued: false\n alias: soil_type\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: FieldResearchSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FieldResearchSite\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FieldResearchSite\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: FieldResearchSite\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: FileTypeEnum
"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Metagenome Raw Reads None Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome Bins Compression File None Compressed file containing all metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... Raw Compressed Metagenome Interleaved Paired-End Reads None Raw sequencing reads from a metagenome that is in interleaved paired-end form..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":"name: file type enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Metagenome Raw Reads:\n text: Metagenome Raw Reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^\\.fastq(\\.gz)?$\n Metagenome Raw Read 1:\n text: Metagenome Raw Read 1\n description: Read 1 raw sequencing data, aka forward reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R1\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n Metagenome Raw Read 2:\n text: Metagenome Raw Read 2\n description: Read 2 raw sequencing data, aka reverse reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R2\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n FT ICR-MS Analysis Results:\n text: FT ICR-MS Analysis Results\n description: FT ICR-MS-based molecular formula assignment results table\n GC-MS Metabolomics Results:\n text: GC-MS Metabolomics Results\n description: GC-MS-based metabolite assignment results table\n Metaproteomics Workflow Statistics:\n text: Metaproteomics Workflow Statistics\n description: Aggregate workflow statistics file\n Protein Report:\n text: Protein Report\n description: Filtered protein report file\n Peptide Report:\n text: Peptide Report\n description: Filtered peptide report file\n Unfiltered Metaproteomics Results:\n text: Unfiltered Metaproteomics Results\n description: MSGFjobs and MASIC output file\n Read Count and RPKM:\n text: Read Count and RPKM\n description: Annotation read count and RPKM per feature JSON\n QC non-rRNA R2:\n text: QC non-rRNA R2\n description: QC removed rRNA reads (R2) fastq\n QC non-rRNA R1:\n text: QC non-rRNA R1\n description: QC removed rRNA reads (R1) fastq\n Metagenome Bins:\n text: Metagenome Bins\n description: Metagenome bin contigs fasta\n Metagenome Bins Compression File:\n text: Metagenome Bins Compression File\n description: Compressed file containing all metagenome bins and associated files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_hqmq_bin.zip'\n Metagenome Bins Info File:\n text: Metagenome Bins Info File\n description: File containing version information on the binning workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_bin.info'\n CheckM Statistics:\n text: CheckM Statistics\n description: CheckM statistics report\n Read Based Analysis Info File:\n text: Read Based Analysis Info File\n description: File containing reads based analysis information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: profiler.info\n GTDBTK Bacterial Summary:\n text: GTDBTK Bacterial Summary\n description: GTDBTK bacterial summary\n GTDBTK Archaeal Summary:\n text: GTDBTK Archaeal Summary\n description: GTDBTK archaeal summary\n GOTTCHA2 Krona Plot:\n text: GOTTCHA2 Krona Plot\n description: GOTTCHA2 krona plot HTML file\n GOTTCHA2 Classification Report:\n text: GOTTCHA2 Classification Report\n description: GOTTCHA2 classification report file\n GOTTCHA2 Report Full:\n text: GOTTCHA2 Report Full\n description: GOTTCHA2 report file\n Kraken2 Krona Plot:\n text: Kraken2 Krona Plot\n description: Kraken2 krona plot HTML file\n Centrifuge Krona Plot:\n text: Centrifuge Krona Plot\n description: Centrifuge krona plot HTML file\n Centrifuge output report file:\n text: Centrifuge output report file\n description: Centrifuge output report file\n Kraken2 Classification Report:\n text: Kraken2 Classification Report\n description: Kraken2 output report file\n Kraken2 Taxonomic Classification:\n text: Kraken2 Taxonomic Classification\n description: Kraken2 output read classification file\n Centrifuge Classification Report:\n text: Centrifuge Classification Report\n description: Centrifuge output report file\n Centrifuge Taxonomic Classification:\n text: Centrifuge Taxonomic Classification\n description: Centrifuge output read classification file\n Structural Annotation GFF:\n text: Structural Annotation GFF\n description: GFF3 format file with structural annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation.gff'\n Structural Annotation Stats Json:\n text: Structural Annotation Stats Json\n description: Structural annotations stats json\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation_stats.json'\n Functional Annotation GFF:\n text: Functional Annotation GFF\n description: GFF3 format file with functional annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_functional_annotation.gff'\n Annotation Info File:\n text: Annotation Info File\n description: File containing annotation info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_imgap.info'\n Annotation Amino Acid FASTA:\n text: Annotation Amino Acid FASTA\n description: FASTA amino acid file for annotated proteins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_proteins.faa'\n Annotation Enzyme Commission:\n text: Annotation Enzyme Commission\n description: Tab delimited file for EC annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ec.tsv'\n Annotation KEGG Orthology:\n text: Annotation KEGG Orthology\n description: Tab delimited file for KO annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko.tsv'\n Assembly Info File:\n text: Assembly Info File\n description: File containing assembly info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: README.txt\n Assembly Coverage BAM:\n text: Assembly Coverage BAM\n description: Sorted bam file of reads mapping back to the final assembly\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped.sam.gz'\n Assembly AGP:\n text: Assembly AGP\n description: An AGP format file that describes the assembly\n Assembly Scaffolds:\n text: Assembly Scaffolds\n description: Final assembly scaffolds fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_assembly.contigs.fasta'\n Assembly Contigs:\n text: Assembly Contigs\n description: Final assembly contigs fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: assembly.contigs.fasta\n Assembly Coverage Stats:\n text: Assembly Coverage Stats\n description: Assembled contigs coverage information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n Contig Mapping File:\n text: Contig Mapping File\n description: Contig mappings between contigs and scaffolds\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_contig_names_mapping.tsv'\n Error Corrected Reads:\n text: Error Corrected Reads\n description: Error corrected reads fastq\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: input.corr.fastq.gz\n Filtered Sequencing Reads:\n text: Filtered Sequencing Reads\n description: Reads QC result fastq (clean data)\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n Read Filtering Info File:\n text: Read Filtering Info File\n description: File containing read filtering information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_readsQC.info'\n QC Statistics Extended:\n text: QC Statistics Extended\n description: Extended report including methods and results for read filtering\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: /.+?(?=filter)/filtered-report.txt\n QC Statistics:\n text: QC Statistics\n description: Reads QC summary statistics\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_filterStats2.txt'\n TIGRFam Annotation GFF:\n text: TIGRFam Annotation GFF\n description: GFF3 format file with TIGRfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_tigrfam.gff'\n CRT Annotation GFF:\n text: CRT Annotation GFF\n description: GFF3 format file with CRT\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.gff'\n Genemark Annotation GFF:\n text: Genemark Annotation GFF\n description: GFF3 format file with Genemark\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_genemark.gff'\n Prodigal Annotation GFF:\n text: Prodigal Annotation GFF\n description: GFF3 format file with Prodigal\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_prodigal.gff'\n TRNA Annotation GFF:\n text: TRNA Annotation GFF\n description: GFF3 format file with TRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_trna.gff'\n Misc Annotation GFF:\n text: Misc Annotation GFF\n description: GFF3 format file with Misc\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n RFAM Annotation GFF:\n text: RFAM Annotation GFF\n description: GFF3 format file with RFAM\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam.gff'\n TMRNA Annotation GFF:\n text: TMRNA Annotation GFF\n description: GFF3 format file with TMRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n Crispr Terms:\n text: Crispr Terms\n description: Crispr Terms\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.crisprs'\n Product Names:\n text: Product Names\n description: Product names file\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_product_names.tsv'\n Gene Phylogeny tsv:\n text: Gene Phylogeny tsv\n description: Gene Phylogeny tsv\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_gene_phylogeny.tsv'\n Scaffold Lineage tsv:\n text: Scaffold Lineage tsv\n description: phylogeny at the scaffold level\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_scaffold_lineage.tsv'\n Clusters of Orthologous Groups (COG) Annotation GFF:\n text: Clusters of Orthologous Groups (COG) Annotation GFF\n description: GFF3 format file with COGs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cog.gff'\n KO_EC Annotation GFF:\n text: KO_EC Annotation GFF\n description: GFF3 format file with KO_EC\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko_ec.gff'\n CATH FunFams (Functional Families) Annotation GFF:\n text: CATH FunFams (Functional Families) Annotation GFF\n description: GFF3 format file with CATH FunFams\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cath_funfam.gff'\n SUPERFam Annotation GFF:\n text: SUPERFam Annotation GFF\n description: GFF3 format file with SUPERFam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_supfam.gff'\n SMART Annotation GFF:\n text: SMART Annotation GFF\n description: GFF3 format file with SMART\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_smart.gff'\n Pfam Annotation GFF:\n text: Pfam Annotation GFF\n description: GFF3 format file with Pfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pfam.gff'\n Annotation Statistics:\n text: Annotation Statistics\n description: Annotation statistics report\n Direct Infusion FT ICR-MS Raw Data:\n text: Direct Infusion FT ICR-MS Raw Data\n description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n mass spectrometry raw data acquired in broadband full scan mode\n Raw Compressed Metagenome Interleaved Paired-End Reads:\n text: Raw Compressed Metagenome Interleaved Paired-End Reads\n description: Raw sequencing reads from a metagenome that is in interleaved paired-end\n format and compressed using GNU zip format.\n\nURI: FilterTypeEnum
"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":"name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n particulate air filter:\n text: particulate air filter\n chemical air filter:\n text: chemical air filter\n low-MERV pleated media:\n text: low-MERV pleated media\n HEPA:\n text: HEPA\n electrostatic:\n text: electrostatic\n gas-phase or ultraviolet air treatments:\n text: gas-phase or ultraviolet air treatments\n\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: FloorCondEnum
"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":"name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: FloorFinishMatEnum
"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":"name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n tile:\n text: tile\n wood strip or parquet:\n text: wood strip or parquet\n carpet:\n text: carpet\n rug:\n text: rug\n laminate wood:\n text: laminate wood\n lineoleum:\n text: lineoleum\n vinyl composition tile:\n text: vinyl composition tile\n sheet vinyl:\n text: sheet vinyl\n stone:\n text: stone\n bamboo:\n text: bamboo\n cork:\n text: cork\n terrazo:\n text: terrazo\n concrete:\n text: concrete\n none:\n text: none\n sealed:\n text: sealed\n clear finish:\n text: clear finish\n paint:\n text: paint\n none or unfinished:\n text: none or unfinished\n\nURI: FloorStrucEnum
"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":"name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n balcony:\n text: balcony\n floating floor:\n text: floating floor\n glass floor:\n text: glass floor\n raised floor:\n text: raised floor\n sprung floor:\n text: sprung floor\n wood-framed:\n text: wood-framed\n concrete:\n text: concrete\n\nURI: FloorWaterMoldEnum
"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":"name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mold odor:\n text: mold odor\n wet floor:\n text: wet floor\n water stains:\n text: water stains\n wall discoloration:\n text: wall discoloration\n floor discoloration:\n text: floor discoloration\n ceiling discoloration:\n text: ceiling discoloration\n peeling paint or wallpaper:\n text: peeling paint or wallpaper\n bulging walls:\n text: bulging walls\n condensation:\n text: condensation\n\nURI: FreqCleanEnum
"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":"name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Daily:\n text: Daily\n Weekly:\n text: Weekly\n Monthly:\n text: Monthly\n Quarterly:\n text: Quarterly\n Annually:\n text: Annually\n other:\n text: other\n\nAn assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods
URI: nmdc:FunctionalAnnotation
classDiagram\n class FunctionalAnnotation\n FunctionalAnnotation : has_function\n\n FunctionalAnnotation : subject\n\n FunctionalAnnotation --|> GeneProduct : subject\n\n FunctionalAnnotation : was_generated_by\n\n FunctionalAnnotation --|> MetagenomeAnnotationActivity : was_generated_by\n\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows.\n In the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nnotes:\n- move id slot usage patterns to has_function slot usage?\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\nslot_usage:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n domain_of:\n - FunctionalAnnotation\n type:\n name: type\n description: TODO\n range: OntologyClass\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows.\n In the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nnotes:\n- move id slot usage patterns to has_function slot usage?\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n domain_of:\n - FunctionalAnnotation\n type:\n name: type\n description: TODO\n range: OntologyClass\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\nattributes:\n has_function:\n name: has_function\n notes:\n - this slot had been called id\n - Still missing patterns for COG and RetroRules.\n - These patterns aren't tied to the listed prefixes. A discussion about that possibility\n had been started, including the question of whether these lists are intended\n to be open examples or closed\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_function\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: string\n pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subject\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: GeneProduct\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotation\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: MetagenomeAnnotationActivity\n\nURI: nmdc:FunctionalAnnotationAggMember
classDiagram\n class FunctionalAnnotationAggMember\n FunctionalAnnotationAggMember : count\n\n FunctionalAnnotationAggMember : gene_function_id\n\n FunctionalAnnotationAggMember : metagenome_annotation_id\n\n FunctionalAnnotationAggMember --|> WorkflowExecutionActivity : metagenome_annotation_id\n\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- metagenome_annotation_id\n- gene_function_id\n- count\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n metagenome_annotation_id:\n name: metagenome_annotation_id\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metagenome_annotation_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: WorkflowExecutionActivity\n gene_function_id:\n name: gene_function_id\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_function_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: uriorcurie\n count:\n name: count\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: count\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: integer\n\nAbstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
URI: nmdc:FunctionalAnnotationTerm
classDiagram\n class FunctionalAnnotationTerm\n OntologyClass <|-- FunctionalAnnotationTerm\n\n\n FunctionalAnnotationTerm <|-- Pathway\n FunctionalAnnotationTerm <|-- Reaction\n FunctionalAnnotationTerm <|-- OrthologyGroup\n\n\n FunctionalAnnotationTerm : alternative_identifiers\n\n FunctionalAnnotationTerm : description\n\n FunctionalAnnotationTerm : id\n\n FunctionalAnnotationTerm : name\n\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: FunctionalAnnotationTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FunctionalAnnotationTerm\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FunctionalAnnotationTerm\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: FunctionalAnnotationTerm\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: FurnitureEnum
"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":"name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n chair:\n text: chair\n desks:\n text: desks\n\nURI: GenderRestroomEnum
"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":"name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n all gender:\n text: all gender\n female:\n text: female\n gender neurtral:\n text: gender neurtral\n male:\n text: male\n male and female:\n text: male and female\n unisex:\n text: unisex\n\nA molecule encoded by a gene that has an evolved function
URI: nmdc:GeneProduct
classDiagram\n class GeneProduct\n NamedThing <|-- GeneProduct\n\n GeneProduct : alternative_identifiers\n\n GeneProduct : description\n\n GeneProduct : id\n\n GeneProduct : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
PR
UniProtKB
gtpo
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\n\nname: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: GeneProduct\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: GeneProduct\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: GeneProduct\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: GeneProduct\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nA feature localized to an interval along a genome
URI: nmdc:GenomeFeature
classDiagram\n class GenomeFeature\n GenomeFeature : encodes\n\n GenomeFeature --|> GeneProduct : encodes\n\n GenomeFeature : end\n\n GenomeFeature : feature_type\n\n GenomeFeature : phase\n\n GenomeFeature : seqid\n\n GenomeFeature : start\n\n GenomeFeature : strand\n\n GenomeFeature : type\n\n GenomeFeature --|> OntologyClass : type\n\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\nslot_usage:\n seqid:\n name: seqid\n domain_of:\n - GenomeFeature\n required: true\n type:\n name: type\n description: A type from the sequence ontology\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n start:\n name: start\n domain_of:\n - GenomeFeature\n required: true\n end:\n name: end\n domain_of:\n - GenomeFeature\n required: true\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n seqid:\n name: seqid\n domain_of:\n - GenomeFeature\n required: true\n type:\n name: type\n description: A type from the sequence ontology\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n start:\n name: start\n domain_of:\n - GenomeFeature\n required: true\n end:\n name: end\n domain_of:\n - GenomeFeature\n required: true\nattributes:\n encodes:\n name: encodes\n description: The gene product encoded by this feature. Typically this is used\n for a CDS feature or gene feature which will encode a protein. It can also be\n used by a nc transcript ot gene feature that encoded a ncRNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: encodes\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: GeneProduct\n end:\n name: end\n description: The end of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: gff_coordinate\n alias: end\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n feature_type:\n name: feature_type\n description: 'TODO: Yuri to write'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_type\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n phase:\n name: phase\n description: The phase for a coding sequence entity. For example, phase of a CDS\n as represented in a GFF3 with a value of 0, 1 or 2.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:phase\n rank: 1000\n alias: phase\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n minimum_value: 0\n maximum_value: 2\n seqid:\n name: seqid\n description: The ID of the landmark used to establish the coordinate system for\n the current feature.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: seqid\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n required: true\n start:\n name: start\n description: The start of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: gff_coordinate\n alias: start\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n strand:\n name: strand\n description: The strand on which a feature is located. Has a value of '+' (sense\n strand or forward strand) or '-' (anti-sense strand or reverse strand).\n todos:\n - set the range to an enum?\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:strand\n rank: 1000\n alias: strand\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n type:\n name: type\n description: A type from the sequence ontology\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: GenomeFeature\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: OntologyClass\n\nA normalized value for a location on the earth's surface
URI: nmdc:GeolocationValue
classDiagram\n class GeolocationValue\n AttributeValue <|-- GeolocationValue\n\n GeolocationValue : has_raw_value\n\n GeolocationValue : latitude\n\n GeolocationValue : longitude\n\n GeolocationValue : was_generated_by\n\n GeolocationValue --|> Activity : was_generated_by\n\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n domain_of:\n - AttributeValue\n - QuantityValue\n latitude:\n name: latitude\n domain_of:\n - GeolocationValue\n required: true\n longitude:\n name: longitude\n domain_of:\n - GeolocationValue\n required: true\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n domain_of:\n - AttributeValue\n - QuantityValue\n latitude:\n name: latitude\n domain_of:\n - GeolocationValue\n required: true\n longitude:\n name: longitude\n domain_of:\n - GeolocationValue\n required: true\nattributes:\n latitude:\n name: latitude\n description: latitude\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: GeolocationValue\n slot_uri: wgs84:lat\n alias: latitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal degree\n required: true\n longitude:\n name: longitude\n description: longitude\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: GeolocationValue\n slot_uri: wgs84:long\n alias: longitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal degree\n required: true\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: GeolocationValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: GeolocationValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: GrowthHabitEnum
"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":"name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n erect:\n text: erect\n semi-erect:\n text: semi-erect\n spreading:\n text: spreading\n prostrate:\n text: prostrate\n\nURI: HandidnessEnum
"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":"name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ambidexterity:\n text: ambidexterity\n left handedness:\n text: left handedness\n mixed-handedness:\n text: mixed-handedness\n right handedness:\n text: right handedness\n\nURI: HcProducedEnum
"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":"name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil:\n text: Oil\n Gas-Condensate:\n text: Gas-Condensate\n Gas:\n text: Gas\n Bitumen:\n text: Bitumen\n Coalbed Methane:\n text: Coalbed Methane\n other:\n text: other\n\nURI: HcrEnum
"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":"name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil Reservoir:\n text: Oil Reservoir\n Gas Reservoir:\n text: Gas Reservoir\n Oil Sand:\n text: Oil Sand\n Coalbed:\n text: Coalbed\n Shale:\n text: Shale\n Tight Oil Reservoir:\n text: Tight Oil Reservoir\n Tight Gas Reservoir:\n text: Tight Gas Reservoir\n other:\n text: other\n\nURI: HcrGeolAgeEnum
"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: HeatCoolTypeEnum
"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":"name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n radiant system:\n text: radiant system\n heat pump:\n text: heat pump\n forced air system:\n text: forced air system\n steam forced heat:\n text: steam forced heat\n wood stove:\n text: wood stove\n\nURI: HeatDelivLocEnum
"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":"name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: HostSexEnum
"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None male None neuter None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":"name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n female:\n text: female\n hermaphrodite:\n text: hermaphrodite\n male:\n text: male\n neuter:\n text: neuter\n\nAn attribute value representing an image.
URI: nmdc:ImageValue
classDiagram\n class ImageValue\n AttributeValue <|-- ImageValue\n\n ImageValue : description\n\n ImageValue : display_order\n\n ImageValue : has_raw_value\n\n ImageValue : url\n\n ImageValue : was_generated_by\n\n ImageValue --|> Activity : was_generated_by\n\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: ImageValue\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ImageValue\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n display_order:\n name: display_order\n description: When rendering information, this attribute to specify the order in\n which the information should be rendered.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: display_order\n owner: ImageValue\n domain_of:\n - ImageValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: ImageValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: ImageValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: IndoorSpaceEnum
"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":"name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bedroom:\n text: bedroom\n office:\n text: office\n bathroom:\n text: bathroom\n foyer:\n text: foyer\n kitchen:\n text: kitchen\n locker room:\n text: locker room\n hallway:\n text: hallway\n elevator:\n text: elevator\n\nURI: IndoorSurfEnum
"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":"name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n ceiling:\n text: ceiling\n counter top:\n text: counter top\n door:\n text: door\n shelving:\n text: shelving\n vent cover:\n text: vent cover\n window:\n text: window\n wall:\n text: wall\n\nA material entity that is designed to perform a function in a scientific investigation, but is not a reagent[OBI].
URI: nmdc:Instrument
classDiagram\n class Instrument\n NamedThing <|-- Instrument\n\n Instrument : alternative_identifiers\n\n Instrument : description\n\n Instrument : id\n\n Instrument : name\n\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent[OBI].\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000485\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent[OBI].\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000485\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Instrument\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Instrument\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Instrument\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Instrument\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:InstrumentValue
classDiagram\n class InstrumentValue\n AttributeValue <|-- InstrumentValue\n\n InstrumentValue : has_numeric_value\n\n InstrumentValue : has_raw_value\n\n InstrumentValue : has_unit\n\n InstrumentValue : instrument_name\n\n InstrumentValue : was_generated_by\n\n InstrumentValue --|> Activity : was_generated_by\n\n\nname: InstrumentValue\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_unit\n- has_numeric_value\n- instrument_name\n\nname: InstrumentValue\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_unit:\n name: has_unit\n description: Links a QuantityValue to a unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - scale\n mappings:\n - qud:unit\n - schema:unitCode\n rank: 1000\n alias: has_unit\n owner: InstrumentValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n range: unit\n has_numeric_value:\n name: has_numeric_value\n description: Links a quantity value to a number\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: InstrumentValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: float\n instrument_name:\n name: instrument_name\n description: The name of the instrument that was used for processing the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_name\n owner: InstrumentValue\n domain_of:\n - OmicsProcessing\n - InstrumentValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: InstrumentValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: InstrumentValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: IntWallCondEnum
"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":"name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
A value that is an integer
URI: nmdc:IntegerValue
classDiagram\n class IntegerValue\n AttributeValue <|-- IntegerValue\n\n IntegerValue : has_numeric_value\n\n IntegerValue : has_raw_value\n\n IntegerValue : was_generated_by\n\n IntegerValue --|> Activity : was_generated_by\n\n\nname: IntegerValue\ndescription: A value that is an integer\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- has_numeric_value\n\nname: IntegerValue\ndescription: A value that is an integer\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_numeric_value:\n name: has_numeric_value\n description: Links a quantity value to a number\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: IntegerValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: float\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: IntegerValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: IntegerValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: Investigation
"},{"location":"Investigation/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Investigation/#schema-source","title":"Schema Source","text":"URI: JgiContTypeEnum
"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description rna_cont_type Tube or plate (96-well) dna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":"name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plate:\n text: plate\n tube:\n text: tube\n\nA string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: nmdc:LabDevice
classDiagram\n class LabDevice\n LabDevice : activity_speed\n\n LabDevice --|> QuantityValue : activity_speed\n\n LabDevice : activity_temperature\n\n LabDevice --|> QuantityValue : activity_temperature\n\n LabDevice : activity_time\n\n LabDevice --|> QuantityValue : activity_time\n\n LabDevice : device_type\n\n LabDevice --|> DeviceTypeEnum : device_type\n\n\nname: LabDevice\ntitle: Lab device\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- device_type\n- activity_speed\n- activity_temperature\n- activity_time\n\nname: LabDevice\ntitle: Lab device\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n device_type:\n name: device_type\n title: device type\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker type\n rank: 1000\n alias: device_type\n owner: LabDevice\n domain_of:\n - LabDevice\n range: DeviceTypeEnum\n activity_speed:\n name: activity_speed\n title: activity speed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shake_speed\n rank: 1000\n alias: activity_speed\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n activity_temperature:\n name: activity_temperature\n todos:\n - constrain units\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: activity_temperature\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n activity_time:\n name: activity_time\n title: activity time\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shake_time\n rank: 1000\n alias: activity_time\n owner: LabDevice\n domain_of:\n - LabDevice\n range: QuantityValue\n inlined: true\n\nA language code conforming to ISO_639-1
URI: xsd:language
base: str
uri: xsd:language
URI: nmdc:LibraryPreparation
classDiagram\n class LibraryPreparation\n BiosampleProcessing <|-- LibraryPreparation\n\n LibraryPreparation : alternative_identifiers\n\n LibraryPreparation : description\n\n LibraryPreparation : end_date\n\n LibraryPreparation : has_input\n\n LibraryPreparation --|> Biosample : has_input\n\n LibraryPreparation : has_output\n\n LibraryPreparation --|> NamedThing : has_output\n\n LibraryPreparation : id\n\n LibraryPreparation : library_preparation_kit\n\n LibraryPreparation : library_type\n\n LibraryPreparation --|> LibraryTypeEnum : library_type\n\n LibraryPreparation : name\n\n LibraryPreparation : pcr_cycles\n\n LibraryPreparation : processing_institution\n\n LibraryPreparation --|> processing_institution_enum : processing_institution\n\n LibraryPreparation : protocol_link\n\n LibraryPreparation --|> Protocol : protocol_link\n\n LibraryPreparation : start_date\n\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: BiosampleProcessing\nslots:\n- library_preparation_kit\n- library_type\n- pcr_cycles\n- processing_institution\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n library_preparation_kit:\n name: library_preparation_kit\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_preparation_kit\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: string\n library_type:\n name: library_type\n title: library type\n examples:\n - value: DNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_type\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: LibraryTypeEnum\n pcr_cycles:\n name: pcr_cycles\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - OBI:0002475\n rank: 1000\n alias: pcr_cycles\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: integer\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: LibraryPreparation\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: LibraryPreparation\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n required: true\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: LibraryPreparation\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: LibraryPreparation\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: LibraryPreparation\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: LibraryPreparation\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: LibraryPreparation\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: LibraryPreparation\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: LibraryTypeEnum
"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":"name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n\nURI: LightTypeEnum
"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":"name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n natural light:\n text: natural light\n electric light:\n text: electric light\n desk lamp:\n text: desk lamp\n flourescent lights:\n text: flourescent lights\n none:\n text: none\n\nURI: LithologyEnum
"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":"name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Basement:\n text: Basement\n Chalk:\n text: Chalk\n Chert:\n text: Chert\n Coal:\n text: Coal\n Conglomerate:\n text: Conglomerate\n Diatomite:\n text: Diatomite\n Dolomite:\n text: Dolomite\n Limestone:\n text: Limestone\n Sandstone:\n text: Sandstone\n Shale:\n text: Shale\n Siltstone:\n text: Siltstone\n Volcanic:\n text: Volcanic\n other:\n text: other\n\nURI: nmdc:MagBin
classDiagram\n class MagBin\n MagBin : bin_name\n\n MagBin : bin_quality\n\n MagBin : completeness\n\n MagBin : contamination\n\n MagBin : gene_count\n\n MagBin : gtdbtk_class\n\n MagBin : gtdbtk_domain\n\n MagBin : gtdbtk_family\n\n MagBin : gtdbtk_genus\n\n MagBin : gtdbtk_order\n\n MagBin : gtdbtk_phylum\n\n MagBin : gtdbtk_species\n\n MagBin : members_id\n\n MagBin : num_16s\n\n MagBin : num_23s\n\n MagBin : num_5s\n\n MagBin : num_t_rna\n\n MagBin : number_of_contig\n\n MagBin : total_bases\n\n MagBin : type\n\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n bin_name:\n name: bin_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_name\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n bin_quality:\n name: bin_quality\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_quality\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n completeness:\n name: completeness\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: MagBin\n domain_of:\n - MagBin\n range: float\n contamination:\n name: contamination\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: MagBin\n domain_of:\n - MagBin\n range: float\n gene_count:\n name: gene_count\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_count\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n gtdbtk_class:\n name: gtdbtk_class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_class\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_domain:\n name: gtdbtk_domain\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_domain\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_family:\n name: gtdbtk_family\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_family\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_genus:\n name: gtdbtk_genus\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_genus\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_order:\n name: gtdbtk_order\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_order\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_phylum:\n name: gtdbtk_phylum\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_phylum\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_species:\n name: gtdbtk_species\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gtdbtk_species\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n members_id:\n name: members_id\n todos:\n - this slot needs some basic textual annotations and constraints\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: members_id\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n num_16s:\n name: num_16s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_16s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_23s:\n name: num_23s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_23s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_5s:\n name: num_5s\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_5s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n num_t_rna:\n name: num_t_rna\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: num_t_rna\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n number_of_contig:\n name: number_of_contig\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: number_of_contig\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n total_bases:\n name: total_bases\n todos:\n - this slot needs some basic textual annotations and constraints\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: total_bases\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MagBin\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n\nA workflow execution activity that uses computational binning tools to group assembled contigs into genomes
URI: nmdc:MagsAnalysisActivity
classDiagram\n class MagsAnalysisActivity\n WorkflowExecutionActivity <|-- MagsAnalysisActivity\n\n MagsAnalysisActivity : binned_contig_num\n\n MagsAnalysisActivity : ended_at_time\n\n MagsAnalysisActivity : execution_resource\n\n MagsAnalysisActivity : git_url\n\n MagsAnalysisActivity : has_input\n\n MagsAnalysisActivity --|> NamedThing : has_input\n\n MagsAnalysisActivity : has_output\n\n MagsAnalysisActivity --|> NamedThing : has_output\n\n MagsAnalysisActivity : id\n\n MagsAnalysisActivity : input_contig_num\n\n MagsAnalysisActivity : low_depth_contig_num\n\n MagsAnalysisActivity : mags_list\n\n MagsAnalysisActivity --|> MagBin : mags_list\n\n MagsAnalysisActivity : name\n\n MagsAnalysisActivity : part_of\n\n MagsAnalysisActivity --|> NamedThing : part_of\n\n MagsAnalysisActivity : started_at_time\n\n MagsAnalysisActivity : too_short_contig_num\n\n MagsAnalysisActivity : type\n\n MagsAnalysisActivity : unbinned_contig_num\n\n MagsAnalysisActivity : used\n\n MagsAnalysisActivity : version\n\n MagsAnalysisActivity : was_informed_by\n\n MagsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MagsAnalysisActivity\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- input_contig_num\n- binned_contig_num\n- too_short_contig_num\n- low_depth_contig_num\n- unbinned_contig_num\n- mags_list\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MagsAnalysisActivity\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MagsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n input_contig_num:\n name: input_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n binned_contig_num:\n name: binned_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: binned_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n too_short_contig_num:\n name: too_short_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: too_short_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n low_depth_contig_num:\n name: low_depth_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: low_depth_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n unbinned_contig_num:\n name: unbinned_contig_num\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: unbinned_contig_num\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: integer\n mags_list:\n name: mags_list\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: mags_list\n owner: MagsAnalysisActivity\n domain_of:\n - MagsAnalysisActivity\n range: MagBin\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MagsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MagsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MagsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MagsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MagsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MagsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MagsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MaterialContainer
classDiagram\n class MaterialContainer\n MaterialContainer : container_size\n\n MaterialContainer --|> QuantityValue : container_size\n\n MaterialContainer : container_type\n\n MaterialContainer --|> ContainerTypeEnum : container_type\n\n\nname: MaterialContainer\ntitle: Material container\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- container_size\n- container_type\n\nname: MaterialContainer\ntitle: Material container\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n container_size:\n name: container_size\n title: container size\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: container_size\n owner: MaterialContainer\n domain_of:\n - MaterialContainer\n range: QuantityValue\n inlined: true\n container_type:\n name: container_type\n title: container type\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: container_type\n owner: MaterialContainer\n domain_of:\n - MaterialContainer\n range: ContainerTypeEnum\n\nURI: nmdc:MaterialEntity
classDiagram\n class MaterialEntity\n NamedThing <|-- MaterialEntity\n\n\n MaterialEntity <|-- Biosample\n MaterialEntity <|-- ProcessedSample\n MaterialEntity <|-- AnalyticalSample\n MaterialEntity <|-- Site\n\n\n MaterialEntity : alternative_identifiers\n\n MaterialEntity : description\n\n MaterialEntity : id\n\n MaterialEntity : name\n\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialEntity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialEntity\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MaterialEntity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:MaterialSample
classDiagram\n class MaterialSample\n NamedThing <|-- MaterialSample\n\n MaterialSample : alternative_identifiers\n\n MaterialSample : description\n\n MaterialSample : id\n\n MaterialSample : name\n\n\nname: MaterialSample\ntitle: Material sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material entity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MaterialSample\ntitle: Material sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material entity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:matsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MaterialSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OBI:0000744
classDiagram\n class MaterialSamplingActivity\n MaterialSamplingActivity : amount_collected\n\n MaterialSamplingActivity --|> QuantityValue : amount_collected\n\n MaterialSamplingActivity : collected_into\n\n MaterialSamplingActivity --|> MaterialContainer : collected_into\n\n MaterialSamplingActivity : material_output\n\n MaterialSamplingActivity --|> MaterialSample : material_output\n\n MaterialSamplingActivity : sampling_method\n\n MaterialSamplingActivity --|> SamplingMethodEnum : sampling_method\n\n\nname: MaterialSamplingActivity\ntitle: Material sampling activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weighing-activity\nslots:\n- amount_collected\n- collected_into\n- material_output\n- sampling_method\nslot_usage:\n amount_collected:\n name: amount_collected\n aliases:\n - weighing-activity.weight\n domain_of:\n - MaterialSamplingActivity\n collected_into:\n name: collected_into\n aliases:\n - weighing-activity.contanier\n domain_of:\n - MaterialSamplingActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:6\n aliases:\n - weighing-activity.id\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nclass_uri: OBI:0000744\n\nname: MaterialSamplingActivity\ntitle: Material sampling activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weighing-activity\nslot_usage:\n amount_collected:\n name: amount_collected\n aliases:\n - weighing-activity.weight\n domain_of:\n - MaterialSamplingActivity\n collected_into:\n name: collected_into\n aliases:\n - weighing-activity.contanier\n domain_of:\n - MaterialSamplingActivity\n material_output:\n name: material_output\n examples:\n - value: somextract:6\n aliases:\n - weighing-activity.id\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\nattributes:\n amount_collected:\n name: amount_collected\n title: amount collected\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.weight\n rank: 1000\n alias: amount_collected\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: QuantityValue\n inlined: true\n collected_into:\n name: collected_into\n title: collected into\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.contanier\n rank: 1000\n alias: collected_into\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: MaterialContainer\n inlined: true\n material_output:\n name: material_output\n title: material output\n examples:\n - value: somextract:6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weighing-activity.id\n rank: 1000\n alias: material_output\n owner: MaterialSamplingActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\n sampling_method:\n name: sampling_method\n title: sampling method\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sampling_method\n owner: MaterialSamplingActivity\n domain_of:\n - MaterialSamplingActivity\n range: SamplingMethodEnum\nclass_uri: OBI:0000744\n\nURI: MechStrucEnum
"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":"name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n subway:\n text: subway\n coach:\n text: coach\n carriage:\n text: carriage\n elevator:\n text: elevator\n escalator:\n text: escalator\n boat:\n text: boat\n train:\n text: train\n car:\n text: car\n bus:\n text: bus\n\nThis is used to link a metabolomics analysis workflow to a specific metabolite
URI: nmdc:MetaboliteQuantification
classDiagram\n class MetaboliteQuantification\n MetaboliteQuantification : alternative_identifiers\n\n MetaboliteQuantification : highest_similarity_score\n\n MetaboliteQuantification : metabolite_quantified\n\n MetaboliteQuantification --|> ChemicalEntity : metabolite_quantified\n\n\nname: MetaboliteQuantification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_quantified\n\nname: MetaboliteQuantification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: MetaboliteQuantification\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n highest_similarity_score:\n name: highest_similarity_score\n todos:\n - Yuri to fill in description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: highest_similarity_score\n owner: MetaboliteQuantification\n domain_of:\n - MetaboliteQuantification\n range: float\n metabolite_quantified:\n name: metabolite_quantified\n description: the specific metabolite identifier\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metabolite_quantified\n owner: MetaboliteQuantification\n domain_of:\n - MetaboliteQuantification\n range: ChemicalEntity\n\nURI: nmdc:MetabolomicsAnalysisActivity
classDiagram\n class MetabolomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetabolomicsAnalysisActivity\n\n MetabolomicsAnalysisActivity : ended_at_time\n\n MetabolomicsAnalysisActivity : execution_resource\n\n MetabolomicsAnalysisActivity : git_url\n\n MetabolomicsAnalysisActivity : has_calibration\n\n MetabolomicsAnalysisActivity : has_input\n\n MetabolomicsAnalysisActivity --|> NamedThing : has_input\n\n MetabolomicsAnalysisActivity : has_metabolite_quantifications\n\n MetabolomicsAnalysisActivity --|> MetaboliteQuantification : has_metabolite_quantifications\n\n MetabolomicsAnalysisActivity : has_output\n\n MetabolomicsAnalysisActivity --|> NamedThing : has_output\n\n MetabolomicsAnalysisActivity : id\n\n MetabolomicsAnalysisActivity : name\n\n MetabolomicsAnalysisActivity : part_of\n\n MetabolomicsAnalysisActivity --|> NamedThing : part_of\n\n MetabolomicsAnalysisActivity : started_at_time\n\n MetabolomicsAnalysisActivity : type\n\n MetabolomicsAnalysisActivity : used\n\n MetabolomicsAnalysisActivity : version\n\n MetabolomicsAnalysisActivity : was_informed_by\n\n MetabolomicsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MetabolomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_calibration\n- has_metabolite_quantifications\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetabolomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_calibration:\n name: has_calibration\n description: A reference to a file that holds calibration information.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_calibration\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n - NomAnalysisActivity\n range: string\n has_metabolite_quantifications:\n name: has_metabolite_quantifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_metabolite_quantifications\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n range: MetaboliteQuantification\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetabolomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nThis documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).
Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).
All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.
Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/
"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.
To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC schema includes environmental descriptors from the GSC MIxS standards.
Explore how to create a MIxS-compliant sample metadata spreadsheet
Review our example spreadsheet with sample metadata that has been converted to be compliant with the MIxS Soil environment package. Note that not all non-mandatory terms from the MIxs Soil package were relevant for these example samples, and hence were omitted for clarity.
Basic sample spreadsheet (Tab 1 - before conversion to MIxS)
MIxS-compliant soil spreadsheet (Tab 2 - converted to MIxS Soil)
Explore the mandatory, unique, and shared descriptors from the MIxS Soil package
Searchable descriptors from all MIxS environmental packages - coming soon!
Learn more about all of the 17 MIxS environmental packages
The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.
Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).
Overview of the GOLD ecosystem paths
Ecosystem describes biosamples using three different broadest contexts, namely environmental, engineered, and host-associated.
Ecosystem category subdivides the ecosystem into categories, such as aquatic or terrestrial.
Ecosystem type classifies those categories into types, such as freshwater or marine, cave, desert, soil, etc.
Ecosystem subtype allows for additional environmental context or boundaries.
Specific ecosystem that describes the environment that directly influences the sample or the environmental material itself.
Explore how to map sample environments using the GOLD ecosystem classification
Learn more about the GOLD ecosystem paths using an interactive visualization tool.
Review a step-by-step example of how to assign the GOLD ecosystem classification to a lake sediment sample.
The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.
EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.
MIxS: env_broad_scale (a.k.a. Biome): The major environmental system that the sample or specimen came from. Often, the value for this term comes from EnvO\u2019s biome hierarchy, and is similar to GOLD\u2019s Ecosystem category.
MIxS: env_local_scale (a.k.a. Feature): A more direct expression of the sample or specimen\u2019s local vicinity, which likely has a significant influence on the sample or specimen. Possible values are listed in EnvO\u2019s astronomical body part hierarchy, which is similar to GOLD\u2019s Ecosystem type/subtype.
MIxS: env_medium (a.k.a. material): The environmental material(s) immediately surrounding your sample or specimen prior to sampling. Examples of this are found in EnvO\u2019s environmental material hierarchy, and is similar to GOLD\u2019s Specific ecosystem.
Explore how to map sample environments using the EnvO ecosystem classification
Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.
env_broad_scale (Biome)
Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.
env_local_scale (Feature)
Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.
env_medium (Material)
Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.
Therefore, the EnvO triad for oligotrophic lake sediment is:
Env_broad_scale: freshwater lake biome [ENVO_01000252]
Env_local_scale: oligotrophic lake [ENVO_01000774]
Env_medium: lake sediment [ENVO_00000546]
"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.
Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.
"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.
"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC schema can be found here.
For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.
"},{"location":"MetagenomeAnnotationActivity/","title":"Class: MetagenomeAnnotationActivity","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
URI: nmdc:MetagenomeAnnotationActivity
classDiagram\n class MetagenomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetagenomeAnnotationActivity\n\n MetagenomeAnnotationActivity : ended_at_time\n\n MetagenomeAnnotationActivity : execution_resource\n\n MetagenomeAnnotationActivity : git_url\n\n MetagenomeAnnotationActivity : gold_analysis_project_identifiers\n\n MetagenomeAnnotationActivity : has_input\n\n MetagenomeAnnotationActivity --|> NamedThing : has_input\n\n MetagenomeAnnotationActivity : has_output\n\n MetagenomeAnnotationActivity --|> NamedThing : has_output\n\n MetagenomeAnnotationActivity : id\n\n MetagenomeAnnotationActivity : name\n\n MetagenomeAnnotationActivity : part_of\n\n MetagenomeAnnotationActivity --|> NamedThing : part_of\n\n MetagenomeAnnotationActivity : started_at_time\n\n MetagenomeAnnotationActivity : type\n\n MetagenomeAnnotationActivity : used\n\n MetagenomeAnnotationActivity : version\n\n MetagenomeAnnotationActivity : was_informed_by\n\n MetagenomeAnnotationActivity --|> Activity : was_informed_by\n\n\nname: MetagenomeAnnotationActivity\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeAnnotationActivity\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeAnnotationActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_analysis_project_identifiers\n owner: MetagenomeAnnotationActivity\n domain_of:\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n range: external_identifier\n pattern: ^gold:Ga[0-9]+$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeAnnotationActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeAnnotationActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeAnnotationActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n\nA workflow execution activity that converts sequencing reads into an assembled metagenome.
URI: nmdc:MetagenomeAssembly
classDiagram\n class MetagenomeAssembly\n WorkflowExecutionActivity <|-- MetagenomeAssembly\n\n MetagenomeAssembly : asm_score\n\n MetagenomeAssembly : contig_bp\n\n MetagenomeAssembly : contigs\n\n MetagenomeAssembly : ctg_l50\n\n MetagenomeAssembly : ctg_l90\n\n MetagenomeAssembly : ctg_logsum\n\n MetagenomeAssembly : ctg_max\n\n MetagenomeAssembly : ctg_n50\n\n MetagenomeAssembly : ctg_n90\n\n MetagenomeAssembly : ctg_powsum\n\n MetagenomeAssembly : ended_at_time\n\n MetagenomeAssembly : execution_resource\n\n MetagenomeAssembly : gap_pct\n\n MetagenomeAssembly : gc_avg\n\n MetagenomeAssembly : gc_std\n\n MetagenomeAssembly : git_url\n\n MetagenomeAssembly : has_input\n\n MetagenomeAssembly --|> NamedThing : has_input\n\n MetagenomeAssembly : has_output\n\n MetagenomeAssembly --|> NamedThing : has_output\n\n MetagenomeAssembly : id\n\n MetagenomeAssembly : insdc_assembly_identifiers\n\n MetagenomeAssembly : name\n\n MetagenomeAssembly : num_aligned_reads\n\n MetagenomeAssembly : num_input_reads\n\n MetagenomeAssembly : part_of\n\n MetagenomeAssembly --|> NamedThing : part_of\n\n MetagenomeAssembly : scaf_bp\n\n MetagenomeAssembly : scaf_l50\n\n MetagenomeAssembly : scaf_l90\n\n MetagenomeAssembly : scaf_l_gt50k\n\n MetagenomeAssembly : scaf_logsum\n\n MetagenomeAssembly : scaf_max\n\n MetagenomeAssembly : scaf_n50\n\n MetagenomeAssembly : scaf_n90\n\n MetagenomeAssembly : scaf_n_gt50k\n\n MetagenomeAssembly : scaf_pct_gt50k\n\n MetagenomeAssembly : scaf_powsum\n\n MetagenomeAssembly : scaffolds\n\n MetagenomeAssembly : started_at_time\n\n MetagenomeAssembly : type\n\n MetagenomeAssembly : used\n\n MetagenomeAssembly : version\n\n MetagenomeAssembly : was_informed_by\n\n MetagenomeAssembly --|> Activity : was_informed_by\n\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeAssembly\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeAssembly\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeAssembly\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeAssembly\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAssembly\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAssembly\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeAssembly\n domain_of:\n - Activity\n range: string\n\nInitial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
URI: nmdc:MetagenomeSequencingActivity
classDiagram\n class MetagenomeSequencingActivity\n WorkflowExecutionActivity <|-- MetagenomeSequencingActivity\n\n MetagenomeSequencingActivity : ended_at_time\n\n MetagenomeSequencingActivity : execution_resource\n\n MetagenomeSequencingActivity : git_url\n\n MetagenomeSequencingActivity : has_input\n\n MetagenomeSequencingActivity --|> NamedThing : has_input\n\n MetagenomeSequencingActivity : has_output\n\n MetagenomeSequencingActivity --|> NamedThing : has_output\n\n MetagenomeSequencingActivity : id\n\n MetagenomeSequencingActivity : name\n\n MetagenomeSequencingActivity : part_of\n\n MetagenomeSequencingActivity --|> NamedThing : part_of\n\n MetagenomeSequencingActivity : started_at_time\n\n MetagenomeSequencingActivity : type\n\n MetagenomeSequencingActivity : used\n\n MetagenomeSequencingActivity : version\n\n MetagenomeSequencingActivity : was_informed_by\n\n MetagenomeSequencingActivity --|> Activity : was_informed_by\n\n\nname: MetagenomeSequencingActivity\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetagenomeSequencingActivity\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetagenomeSequencingActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetagenomeSequencingActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetagenomeSequencingActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetagenomeSequencingActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeSequencingActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeSequencingActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeSequencingActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetagenomeSequencingActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetaproteomicsAnalysisActivity
classDiagram\n class MetaproteomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetaproteomicsAnalysisActivity\n\n MetaproteomicsAnalysisActivity : ended_at_time\n\n MetaproteomicsAnalysisActivity : execution_resource\n\n MetaproteomicsAnalysisActivity : git_url\n\n MetaproteomicsAnalysisActivity : has_input\n\n MetaproteomicsAnalysisActivity --|> NamedThing : has_input\n\n MetaproteomicsAnalysisActivity : has_output\n\n MetaproteomicsAnalysisActivity --|> NamedThing : has_output\n\n MetaproteomicsAnalysisActivity : has_peptide_quantifications\n\n MetaproteomicsAnalysisActivity --|> PeptideQuantification : has_peptide_quantifications\n\n MetaproteomicsAnalysisActivity : id\n\n MetaproteomicsAnalysisActivity : name\n\n MetaproteomicsAnalysisActivity : part_of\n\n MetaproteomicsAnalysisActivity --|> NamedThing : part_of\n\n MetaproteomicsAnalysisActivity : started_at_time\n\n MetaproteomicsAnalysisActivity : type\n\n MetaproteomicsAnalysisActivity : used\n\n MetaproteomicsAnalysisActivity : version\n\n MetaproteomicsAnalysisActivity : was_informed_by\n\n MetaproteomicsAnalysisActivity --|> Activity : was_informed_by\n\n\nname: MetaproteomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_peptide_quantifications\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetaproteomicsAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_peptide_quantifications:\n name: has_peptide_quantifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_peptide_quantifications\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - MetaproteomicsAnalysisActivity\n range: PeptideQuantification\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Activity\n alias: used\n owner: MetaproteomicsAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nA metatranscriptome activity that e.g. pools assembly and annotation activity.
URI: nmdc:MetatranscriptomeActivity
classDiagram\n class MetatranscriptomeActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeActivity\n\n MetatranscriptomeActivity : ended_at_time\n\n MetatranscriptomeActivity : execution_resource\n\n MetatranscriptomeActivity : git_url\n\n MetatranscriptomeActivity : has_input\n\n MetatranscriptomeActivity --|> NamedThing : has_input\n\n MetatranscriptomeActivity : has_output\n\n MetatranscriptomeActivity --|> NamedThing : has_output\n\n MetatranscriptomeActivity : id\n\n MetatranscriptomeActivity : name\n\n MetatranscriptomeActivity : part_of\n\n MetatranscriptomeActivity --|> NamedThing : part_of\n\n MetatranscriptomeActivity : started_at_time\n\n MetatranscriptomeActivity : type\n\n MetatranscriptomeActivity : used\n\n MetatranscriptomeActivity : version\n\n MetatranscriptomeActivity : was_informed_by\n\n MetatranscriptomeActivity --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeActivity\ndescription: A metatranscriptome activity that e.g. pools assembly and annotation\n activity.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeActivity\ndescription: A metatranscriptome activity that e.g. pools assembly and annotation\n activity.\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetatranscriptomeAnnotationActivity
classDiagram\n class MetatranscriptomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeAnnotationActivity\n\n MetatranscriptomeAnnotationActivity : ended_at_time\n\n MetatranscriptomeAnnotationActivity : execution_resource\n\n MetatranscriptomeAnnotationActivity : git_url\n\n MetatranscriptomeAnnotationActivity : gold_analysis_project_identifiers\n\n MetatranscriptomeAnnotationActivity : has_input\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : has_input\n\n MetatranscriptomeAnnotationActivity : has_output\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : has_output\n\n MetatranscriptomeAnnotationActivity : id\n\n MetatranscriptomeAnnotationActivity : name\n\n MetatranscriptomeAnnotationActivity : part_of\n\n MetatranscriptomeAnnotationActivity --|> NamedThing : part_of\n\n MetatranscriptomeAnnotationActivity : started_at_time\n\n MetatranscriptomeAnnotationActivity : type\n\n MetatranscriptomeAnnotationActivity : used\n\n MetatranscriptomeAnnotationActivity : version\n\n MetatranscriptomeAnnotationActivity : was_informed_by\n\n MetatranscriptomeAnnotationActivity --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeAnnotationActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeAnnotationActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_analysis_project_identifiers\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n range: external_identifier\n pattern: ^gold:Ga[0-9]+$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeAnnotationActivity\n domain_of:\n - Activity\n range: string\n\nURI: nmdc:MetatranscriptomeAssembly
classDiagram\n class MetatranscriptomeAssembly\n WorkflowExecutionActivity <|-- MetatranscriptomeAssembly\n\n MetatranscriptomeAssembly : asm_score\n\n MetatranscriptomeAssembly : contig_bp\n\n MetatranscriptomeAssembly : contigs\n\n MetatranscriptomeAssembly : ctg_l50\n\n MetatranscriptomeAssembly : ctg_l90\n\n MetatranscriptomeAssembly : ctg_logsum\n\n MetatranscriptomeAssembly : ctg_max\n\n MetatranscriptomeAssembly : ctg_n50\n\n MetatranscriptomeAssembly : ctg_n90\n\n MetatranscriptomeAssembly : ctg_powsum\n\n MetatranscriptomeAssembly : ended_at_time\n\n MetatranscriptomeAssembly : execution_resource\n\n MetatranscriptomeAssembly : gap_pct\n\n MetatranscriptomeAssembly : gc_avg\n\n MetatranscriptomeAssembly : gc_std\n\n MetatranscriptomeAssembly : git_url\n\n MetatranscriptomeAssembly : has_input\n\n MetatranscriptomeAssembly --|> NamedThing : has_input\n\n MetatranscriptomeAssembly : has_output\n\n MetatranscriptomeAssembly --|> NamedThing : has_output\n\n MetatranscriptomeAssembly : id\n\n MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n MetatranscriptomeAssembly : name\n\n MetatranscriptomeAssembly : num_aligned_reads\n\n MetatranscriptomeAssembly : num_input_reads\n\n MetatranscriptomeAssembly : part_of\n\n MetatranscriptomeAssembly --|> NamedThing : part_of\n\n MetatranscriptomeAssembly : scaf_bp\n\n MetatranscriptomeAssembly : scaf_l50\n\n MetatranscriptomeAssembly : scaf_l90\n\n MetatranscriptomeAssembly : scaf_l_gt50k\n\n MetatranscriptomeAssembly : scaf_logsum\n\n MetatranscriptomeAssembly : scaf_max\n\n MetatranscriptomeAssembly : scaf_n50\n\n MetatranscriptomeAssembly : scaf_n90\n\n MetatranscriptomeAssembly : scaf_n_gt50k\n\n MetatranscriptomeAssembly : scaf_pct_gt50k\n\n MetatranscriptomeAssembly : scaf_powsum\n\n MetatranscriptomeAssembly : scaffolds\n\n MetatranscriptomeAssembly : started_at_time\n\n MetatranscriptomeAssembly : type\n\n MetatranscriptomeAssembly : used\n\n MetatranscriptomeAssembly : version\n\n MetatranscriptomeAssembly : was_informed_by\n\n MetatranscriptomeAssembly --|> Activity : was_informed_by\n\n\nname: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: MetatranscriptomeAssembly\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: MetatranscriptomeAssembly\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: MetatranscriptomeAssembly\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: MetatranscriptomeAssembly\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: MetatranscriptomeAssembly\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAssembly\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAssembly\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: MetatranscriptomeAssembly\n domain_of:\n - Activity\n range: string\n\nURI: MixsEnvironmentalTriad
"},{"location":"MixsEnvironmentalTriad/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsEnvironmentalTriad/#schema-source","title":"Schema Source","text":"URI: MixsExtension
"},{"location":"MixsExtension/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MixsExtension/#schema-source","title":"Schema Source","text":"Schema for National Microbiome Data Collaborative (NMDC). This schema is organized into multiple modules, such as:
URI: https://w3id.org/nmdc/nmdc
"},{"location":"NamedThing/","title":"Class: NamedThing","text":"a databased entity or concept/class
URI: nmdc:NamedThing
classDiagram\n class NamedThing\n NamedThing <|-- DataObject\n NamedThing <|-- Study\n NamedThing <|-- MaterialEntity\n NamedThing <|-- PlannedProcess\n NamedThing <|-- OntologyClass\n NamedThing <|-- Instrument\n NamedThing <|-- GeneProduct\n NamedThing <|-- MaterialSample\n\n NamedThing : alternative_identifiers\n\n NamedThing : description\n\n NamedThing : id\n\n NamedThing : name\n\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: NamedThing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NamedThing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NamedThing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: NamedThing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
A URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: nmdc:NomAnalysisActivity
classDiagram\n class NomAnalysisActivity\n WorkflowExecutionActivity <|-- NomAnalysisActivity\n\n NomAnalysisActivity : ended_at_time\n\n NomAnalysisActivity : execution_resource\n\n NomAnalysisActivity : git_url\n\n NomAnalysisActivity : has_calibration\n\n NomAnalysisActivity : has_input\n\n NomAnalysisActivity --|> NamedThing : has_input\n\n NomAnalysisActivity : has_output\n\n NomAnalysisActivity --|> NamedThing : has_output\n\n NomAnalysisActivity : id\n\n NomAnalysisActivity : name\n\n NomAnalysisActivity : part_of\n\n NomAnalysisActivity --|> NamedThing : part_of\n\n NomAnalysisActivity : started_at_time\n\n NomAnalysisActivity : type\n\n NomAnalysisActivity : used\n\n NomAnalysisActivity : version\n\n NomAnalysisActivity : was_informed_by\n\n NomAnalysisActivity --|> Activity : was_informed_by\n\n\nname: NomAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- has_calibration\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n range: string\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: NomAnalysisActivity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n domain_of:\n - Activity\n range: string\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_calibration:\n name: has_calibration\n description: A reference to a file that holds calibration information.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_calibration\n owner: NomAnalysisActivity\n domain_of:\n - MetabolomicsAnalysisActivity\n - NomAnalysisActivity\n range: string\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: NomAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: NomAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: NomAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: NomAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: NomAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: NomAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NomAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n description: The instrument used to collect the data used in the analysis\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Activity\n alias: used\n owner: NomAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: NucleicAcidSequenceSource
"},{"location":"NucleicAcidSequenceSource/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleicAcidSequenceSource/#schema-source","title":"Schema Source","text":"A URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
URI: OccupDocumentEnum
"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":"name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n automated count:\n text: automated count\n estimate:\n text: estimate\n manual count:\n text: manual count\n videos:\n text: videos\n\nThe methods and processes used to generate omics data from a biosample or organism.
URI: nmdc:OmicsProcessing
classDiagram\n class OmicsProcessing\n PlannedProcess <|-- OmicsProcessing\n\n OmicsProcessing : add_date\n\n OmicsProcessing : alternative_identifiers\n\n OmicsProcessing : chimera_check\n\n OmicsProcessing --|> TextValue : chimera_check\n\n OmicsProcessing : description\n\n OmicsProcessing : end_date\n\n OmicsProcessing : gold_sequencing_project_identifiers\n\n OmicsProcessing : has_input\n\n OmicsProcessing --|> NamedThing : has_input\n\n OmicsProcessing : has_output\n\n OmicsProcessing --|> NamedThing : has_output\n\n OmicsProcessing : id\n\n OmicsProcessing : insdc_experiment_identifiers\n\n OmicsProcessing : instrument_name\n\n OmicsProcessing : mod_date\n\n OmicsProcessing : name\n\n OmicsProcessing : ncbi_project_name\n\n OmicsProcessing : nucl_acid_amp\n\n OmicsProcessing --|> TextValue : nucl_acid_amp\n\n OmicsProcessing : nucl_acid_ext\n\n OmicsProcessing --|> TextValue : nucl_acid_ext\n\n OmicsProcessing : omics_type\n\n OmicsProcessing --|> ControlledTermValue : omics_type\n\n OmicsProcessing : part_of\n\n OmicsProcessing --|> NamedThing : part_of\n\n OmicsProcessing : pcr_cond\n\n OmicsProcessing --|> TextValue : pcr_cond\n\n OmicsProcessing : pcr_primers\n\n OmicsProcessing --|> TextValue : pcr_primers\n\n OmicsProcessing : principal_investigator\n\n OmicsProcessing --|> PersonValue : principal_investigator\n\n OmicsProcessing : processing_institution\n\n OmicsProcessing --|> processing_institution_enum : processing_institution\n\n OmicsProcessing : protocol_link\n\n OmicsProcessing --|> Protocol : protocol_link\n\n OmicsProcessing : samp_vol_we_dna_ext\n\n OmicsProcessing --|> QuantityValue : samp_vol_we_dna_ext\n\n OmicsProcessing : seq_meth\n\n OmicsProcessing --|> TextValue : seq_meth\n\n OmicsProcessing : seq_quality_check\n\n OmicsProcessing --|> TextValue : seq_quality_check\n\n OmicsProcessing : start_date\n\n OmicsProcessing : target_gene\n\n OmicsProcessing --|> TextValue : target_gene\n\n OmicsProcessing : target_subfragment\n\n OmicsProcessing --|> TextValue : target_subfragment\n\n OmicsProcessing : type\n\n\nname: OmicsProcessing\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\ncomments:\n- The ID prefix for objects coming from GOLD will be gold:Gp\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nslots:\n- add_date\n- chimera_check\n- gold_sequencing_project_identifiers\n- has_input\n- has_output\n- insdc_experiment_identifiers\n- instrument_name\n- mod_date\n- ncbi_project_name\n- nucl_acid_amp\n- nucl_acid_ext\n- omics_type\n- part_of\n- pcr_cond\n- pcr_primers\n- principal_investigator\n- processing_institution\n- samp_vol_we_dna_ext\n- seq_meth\n- seq_quality_check\n- target_gene\n- target_subfragment\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n\nname: OmicsProcessing\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\ncomments:\n- The ID prefix for objects coming from GOLD will be gold:Gp\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\nattributes:\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n chimera_check:\n name: chimera_check\n annotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\n description: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised\n of two or more phylogenetically distinct parent sequences.\n title: chimera check software\n examples:\n - value: uchime;v4.1;default parameters\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chimera check software\n rank: 1000\n is_a: sequencing field\n string_serialization: '{software};{version};{parameters}'\n slot_uri: MIXS:0000052\n multivalued: false\n alias: chimera_check\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n gold_sequencing_project_identifiers:\n name: gold_sequencing_project_identifiers\n description: identifiers for corresponding sequencing project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Gp0108335\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: omics_processing_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_sequencing_project_identifiers\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: external_identifier\n pattern: ^gold:Gp[0-9]+$\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: OmicsProcessing\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n multivalued: true\n alias: insdc_experiment_identifiers\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: external_identifier\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n instrument_name:\n name: instrument_name\n description: The name of the instrument that was used for processing the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_name\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n - InstrumentValue\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: string\n ncbi_project_name:\n name: ncbi_project_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_project_name\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: string\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n multivalued: false\n alias: nucl_acid_amp\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n nucl_acid_ext:\n name: nucl_acid_ext\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the material separation to recover\n the nucleic acid fraction from a sample\n title: nucleic acid extraction\n examples:\n - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid extraction\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000037\n multivalued: false\n alias: nucl_acid_ext\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n omics_type:\n name: omics_type\n description: The type of omics data\n notes:\n - was the range string at one point? the values in MongoDB don't look like NMDC\n classes\n examples:\n - value: metatranscriptome\n - value: metagenome\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: omics_type\n owner: OmicsProcessing\n domain_of:\n - OmicsProcessing\n range: ControlledTermValue\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: OmicsProcessing\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n multivalued: false\n alias: pcr_cond\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n multivalued: false\n alias: pcr_primers\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n is_a: attribute\n alias: principal_investigator\n owner: OmicsProcessing\n domain_of:\n - Study\n - OmicsProcessing\n range: PersonValue\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: OmicsProcessing\n domain_of:\n - Extraction\n - LibraryPreparation\n - OmicsProcessing\n range: processing_institution_enum\n samp_vol_we_dna_ext:\n name: samp_vol_we_dna_ext\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\n description: 'Volume (ml) or mass (g) of total collected sample processed for\n DNA extraction. Note: total sample collected should be entered under the term\n Sample Size (MIXS:0000001).'\n title: sample volume or weight for DNA extraction\n examples:\n - value: 1500 milliliter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample volume or weight for DNA extraction\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000111\n multivalued: false\n alias: samp_vol_we_dna_ext\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: QuantityValue\n seq_meth:\n name: seq_meth\n annotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\n description: Sequencing machine used. Where possible the term should be taken\n from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\n title: sequencing method\n examples:\n - value: 454 Genome Sequencer FLX [OBI:0000702]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequencing method\n rank: 1000\n is_a: sequencing field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000050\n multivalued: false\n alias: seq_meth\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n seq_quality_check:\n name: seq_quality_check\n annotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\n description: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or\n chromatograms). Applied only for sequences that are not submitted to SRA,ENA\n or DRA\n title: sequence quality check\n examples:\n - value: none\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sequence quality check\n rank: 1000\n is_a: sequencing field\n string_serialization: '[none|manually edited]'\n slot_uri: MIXS:0000051\n multivalued: false\n alias: seq_quality_check\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n multivalued: false\n alias: target_gene\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n multivalued: false\n alias: target_subfragment\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - OmicsProcessing\n range: TextValue\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: OmicsProcessing\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: OmicsProcessing\n domain_of:\n - PlannedProcess\n range: string\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: OmicsProcessing\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: OmicsProcessing\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:omprc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OmicsProcessing\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OmicsProcessing\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OmicsProcessing\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:OntologyClass
classDiagram\n class OntologyClass\n NamedThing <|-- OntologyClass\n\n\n OntologyClass <|-- EnvironmentalMaterialTerm\n OntologyClass <|-- ChemicalEntity\n OntologyClass <|-- FunctionalAnnotationTerm\n\n\n OntologyClass : alternative_identifiers\n\n OntologyClass : description\n\n OntologyClass : id\n\n OntologyClass : name\n\n\nname: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nname: OntologyClass\nnotes:\n- The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OntologyClass\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OntologyClass\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OntologyClass\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OntologyClass\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OrganismCountEnum
"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":"name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ATP:\n text: ATP\n MPN:\n text: MPN\n other:\n text: other\n\nA set of genes or gene products in which all members are orthologous
URI: nmdc:OrthologyGroup
classDiagram\n class OrthologyGroup\n FunctionalAnnotationTerm <|-- OrthologyGroup\n\n OrthologyGroup : alternative_identifiers\n\n OrthologyGroup : description\n\n OrthologyGroup : id\n\n OrthologyGroup : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CATH
EGGNOG
KEGG.ORTHOLOGY
PANTHER.FAMILY
PFAM
SUPFAM
TIGRFAM
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\n\nname: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: OrthologyGroup\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OrthologyGroup\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OrthologyGroup\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: OrthologyGroup\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: OxyStatSampEnum
"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample oxy_stat_samp"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":"name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aerobic:\n text: aerobic\n anaerobic:\n text: anaerobic\n other:\n text: other\n\nA MIxS package. These can be combined with checklists
URI: Package
"},{"location":"Package/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Package/#schema-source","title":"Schema Source","text":"A pathway is a sequence of steps/reactions carried out by an organism or community of organisms
URI: nmdc:Pathway
classDiagram\n class Pathway\n FunctionalAnnotationTerm <|-- Pathway\n\n Pathway : alternative_identifiers\n\n Pathway : description\n\n Pathway : has_part\n\n Pathway --|> Reaction : has_part\n\n Pathway : id\n\n Pathway : name\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG_PATHWAY
COG
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nslots:\n- has_part\n\nname: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n has_part:\n name: has_part\n description: A pathway can be broken down to a series of reaction step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: has_part\n owner: Pathway\n domain_of:\n - Pathway\n range: Reaction\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Pathway\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pathway\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pathway\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Pathway\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information
URI: nmdc:PeptideQuantification
classDiagram\n class PeptideQuantification\n PeptideQuantification : all_proteins\n\n PeptideQuantification --|> GeneProduct : all_proteins\n\n PeptideQuantification : best_protein\n\n PeptideQuantification --|> GeneProduct : best_protein\n\n PeptideQuantification : min_q_value\n\n PeptideQuantification : peptide_sequence\n\n PeptideQuantification : peptide_spectral_count\n\n PeptideQuantification : peptide_sum_masic_abundance\n\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: all_proteins\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n min_q_value:\n name: min_q_value\n description: smallest Q-Value associated with the peptide sequence as provided\n by MSGFPlus tool\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - OBI:0001442\n rank: 1000\n alias: min_q_value\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: float\n peptide_sequence:\n name: peptide_sequence\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: string\n peptide_spectral_count:\n name: peptide_spectral_count\n description: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_spectral_count\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n peptide_sum_masic_abundance:\n name: peptide_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the peptide sequence from a given LC-MS/MS data file using the\n MASIC tool\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sum_masic_abundance\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n\nAn attribute value representing a person
URI: nmdc:PersonValue
classDiagram\n class PersonValue\n AttributeValue <|-- PersonValue\n\n PersonValue : email\n\n PersonValue : has_raw_value\n\n PersonValue : name\n\n PersonValue : orcid\n\n PersonValue : profile_image_url\n\n PersonValue : was_generated_by\n\n PersonValue --|> Activity : was_generated_by\n\n PersonValue : websites\n\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n domain_of:\n - PersonValue\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n domain_of:\n - PersonValue\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n domain_of:\n - AttributeValue\n - QuantityValue\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n domain_of:\n - PersonValue\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n domain_of:\n - PersonValue\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n domain_of:\n - AttributeValue\n - QuantityValue\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\nattributes:\n email:\n name: email\n annotations:\n display_hint:\n tag: display_hint\n value: Email address for this person.\n description: An email address for an entity such as a person. This should be the\n primary email address used.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: schema:email\n alias: email\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PersonValue\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n orcid:\n name: orcid\n annotations:\n display_hint:\n tag: display_hint\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n description: The ORCID of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: PersonValue\n alias: orcid\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n profile_image_url:\n name: profile_image_url\n description: A url that points to an image of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: PersonValue\n alias: profile_image_url\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n websites:\n name: websites\n description: A list of websites that are associated with the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: websites\n owner: PersonValue\n domain_of:\n - Study\n - PersonValue\n range: string\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: PersonValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: PersonValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: OBI:0000011
classDiagram\n class PlannedProcess\n NamedThing <|-- PlannedProcess\n\n\n PlannedProcess <|-- CollectingBiosamplesFromSite\n PlannedProcess <|-- BiosampleProcessing\n PlannedProcess <|-- OmicsProcessing\n\n\n PlannedProcess : alternative_identifiers\n\n PlannedProcess : description\n\n PlannedProcess : end_date\n\n PlannedProcess : has_input\n\n PlannedProcess --|> NamedThing : has_input\n\n PlannedProcess : has_output\n\n PlannedProcess --|> NamedThing : has_output\n\n PlannedProcess : id\n\n PlannedProcess : name\n\n PlannedProcess : protocol_link\n\n PlannedProcess --|> Protocol : protocol_link\n\n PlannedProcess : start_date\n\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- end_date\n- has_input\n- has_output\n- protocol_link\n- start_date\nclass_uri: OBI:0000011\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: PlannedProcess\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: PlannedProcess\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: PlannedProcess\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: PlannedProcess\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PlannedProcess\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: PlannedProcess\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: PlannedProcess\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nclass_uri: OBI:0000011\n\nURI: PlantGrowthMedEnum
"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":"name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n other artificial liquid medium:\n text: other artificial liquid medium\n other artificial solid medium:\n text: other artificial solid medium\n peat moss:\n text: peat moss\n perlite:\n text: perlite\n pumice:\n text: pumice\n sand:\n text: sand\n soil:\n text: soil\n vermiculite:\n text: vermiculite\n water:\n text: water\n\nURI: PlantSexEnum
"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":"name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Androdioecious:\n text: Androdioecious\n Androecious:\n text: Androecious\n Androgynous:\n text: Androgynous\n Androgynomonoecious:\n text: Androgynomonoecious\n Andromonoecious:\n text: Andromonoecious\n Bisexual:\n text: Bisexual\n Dichogamous:\n text: Dichogamous\n Diclinous:\n text: Diclinous\n Dioecious:\n text: Dioecious\n Gynodioecious:\n text: Gynodioecious\n Gynoecious:\n text: Gynoecious\n Gynomonoecious:\n text: Gynomonoecious\n Hermaphroditic:\n text: Hermaphroditic\n Imperfect:\n text: Imperfect\n Monoclinous:\n text: Monoclinous\n Monoecious:\n text: Monoecious\n Perfect:\n text: Perfect\n Polygamodioecious:\n text: Polygamodioecious\n Polygamomonoecious:\n text: Polygamomonoecious\n Polygamous:\n text: Polygamous\n Protandrous:\n text: Protandrous\n Protogynous:\n text: Protogynous\n Subandroecious:\n text: Subandroecious\n Subdioecious:\n text: Subdioecious\n Subgynoecious:\n text: Subgynoecious\n Synoecious:\n text: Synoecious\n Trimonoecious:\n text: Trimonoecious\n Trioecious:\n text: Trioecious\n Unisexual:\n text: Unisexual\n\nphysical combination of several instances of like material.
URI: nmdc:Pooling
classDiagram\n class Pooling\n BiosampleProcessing <|-- Pooling\n\n Pooling : alternative_identifiers\n\n Pooling : description\n\n Pooling : end_date\n\n Pooling : has_input\n\n Pooling --|> Biosample : has_input\n\n Pooling : has_output\n\n Pooling --|> NamedThing : has_output\n\n Pooling : id\n\n Pooling : name\n\n Pooling : protocol_link\n\n Pooling --|> Protocol : protocol_link\n\n Pooling : start_date\n\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 2\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: BiosampleProcessing\nslot_usage:\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 2\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: Pooling\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: Biosample\n minimum_cardinality: 2\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: Pooling\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n minimum_cardinality: 1\n maximum_cardinality: 1\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Pooling\n domain_of:\n - Extraction\n - PlannedProcess\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Pooling\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pooling\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pooling\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Pooling\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:ProcessedSample
classDiagram\n class ProcessedSample\n MaterialEntity <|-- ProcessedSample\n\n ProcessedSample : alternative_identifiers\n\n ProcessedSample : biomaterial_purity\n\n ProcessedSample --|> QuantityValue : biomaterial_purity\n\n ProcessedSample : description\n\n ProcessedSample : dna_absorb1\n\n ProcessedSample : dna_concentration\n\n ProcessedSample : external_database_identifiers\n\n ProcessedSample : id\n\n ProcessedSample : name\n\n ProcessedSample : nucleic_acid_concentration\n\n ProcessedSample --|> InstrumentValue : nucleic_acid_concentration\n\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\n- nucleic_acid_concentration\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n biomaterial_purity:\n name: biomaterial_purity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biomaterial_purity\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n string_serialization: '{float}'\n alias: dna_absorb1\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: dna_concentration\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n external_database_identifiers:\n name: external_database_identifiers\n description: Link to corresponding identifier in external database\n notes:\n - had tried ranges of external identifier and string\n comments:\n - The value of this field is always a registered CURIE\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - skos:closeMatch\n rank: 1000\n is_a: alternative_identifiers\n abstract: true\n multivalued: true\n alias: external_database_identifiers\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n nucleic_acid_concentration:\n name: nucleic_acid_concentration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: nucleic_acid_concentration\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: InstrumentValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ProcessedSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProcessedSample\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProcessedSample\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: ProcessedSample\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: ProcessingInstitutionEnum
"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":"name: processing_institution_enum\nnotes:\n- This will become the range of processing_institution.omics processing\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n UCSD:\n text: UCSD\n meaning: https://ror.org/0168r3w48\n title: University of California, San Diego\n JGI:\n text: JGI\n meaning: https://ror.org/04xm1d337\n title: Joint Genome Institute\n EMSL:\n text: EMSL\n meaning: https://ror.org/04rc0xn13\n title: Environmental Molecular Sciences Laboratory\n notes:\n - replaces Environmental Molecular Science Laboratory\n - replaces Environmental Molecular Sciences Lab\n Battelle:\n text: Battelle\n meaning: https://ror.org/01h5tnr73\n title: Battelle Memorial Institute\n ANL:\n text: ANL\n meaning: https://ror.org/05gvnxz63\n title: Argonne National Laboratory\n\nURI: ProfilePositionEnum
"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":"name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n summit:\n text: summit\n shoulder:\n text: shoulder\n backslope:\n text: backslope\n footslope:\n text: footslope\n toeslope:\n text: toeslope\n\nThis is used to link a metaproteomics analysis workflow to a specific protein
URI: nmdc:ProteinQuantification
classDiagram\n class ProteinQuantification\n ProteinQuantification : all_proteins\n\n ProteinQuantification --|> GeneProduct : all_proteins\n\n ProteinQuantification : best_protein\n\n ProteinQuantification --|> GeneProduct : best_protein\n\n ProteinQuantification : peptide_sequence_count\n\n ProteinQuantification : protein_spectral_count\n\n ProteinQuantification : protein_sum_masic_abundance\n\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\nslot_usage:\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\nattributes:\n all_proteins:\n name: all_proteins\n description: the grouped list of protein identifiers associated with the peptide\n sequences that were grouped to a best protein\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: all_proteins\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly grouped to its associated\n peptide sequences\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n peptide_sequence_count:\n name: peptide_sequence_count\n description: count of peptide sequences grouped to the best_protein\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_spectral_count:\n name: protein_spectral_count\n description: sum of filter passing MS2 spectra associated with the best protein\n within a given LC-MS/MS data file\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_spectral_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_sum_masic_abundance:\n name: protein_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the best protein from a given LC-MS/MS data file using the MASIC\n tool\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_sum_masic_abundance\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n\nURI: nmdc:Protocol
classDiagram\n class Protocol\n Protocol : name\n\n Protocol : url\n\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: url\n owner: Protocol\n domain_of:\n - Protocol\n - DataObject\n - ImageValue\n range: string\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Protocol\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nURI: QuadPosEnum
"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":"name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n North side:\n text: North side\n West side:\n text: West side\n South side:\n text: South side\n East side:\n text: East side\n\nURI: nmdc:QualityControlReport
classDiagram\n class QualityControlReport\n QualityControlReport : name\n\n QualityControlReport : status\n\n QualityControlReport --|> StatusEnum : status\n\n\nname: QualityControlReport\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- status\n- name\n\nname: QualityControlReport\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n status:\n name: status\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: status\n owner: QualityControlReport\n domain_of:\n - QualityControlReport\n range: StatusEnum\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: QualityControlReport\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nA simple quantity, e.g. 2cm
URI: nmdc:QuantityValue
classDiagram\n class QuantityValue\n AttributeValue <|-- QuantityValue\n\n QuantityValue : has_maximum_numeric_value\n\n QuantityValue : has_minimum_numeric_value\n\n QuantityValue : has_numeric_value\n\n QuantityValue : has_raw_value\n\n QuantityValue : has_unit\n\n QuantityValue : was_generated_by\n\n QuantityValue --|> Activity : was_generated_by\n\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_raw_value\n- has_unit\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n domain_of:\n - AttributeValue\n - QuantityValue\n has_unit:\n name: has_unit\n description: The unit of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n domain_of:\n - AttributeValue\n - QuantityValue\n has_unit:\n name: has_unit\n description: The unit of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\nattributes:\n has_maximum_numeric_value:\n name: has_maximum_numeric_value\n description: The maximum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_maximum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: float\n has_minimum_numeric_value:\n name: has_minimum_numeric_value\n description: The minimum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_minimum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: float\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: false\n alias: has_numeric_value\n owner: QuantityValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n - IntegerValue\n range: double\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: QuantityValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n has_unit:\n name: has_unit\n description: The unit of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_unit\n owner: QuantityValue\n domain_of:\n - InstrumentValue\n - QuantityValue\n range: unit\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: QuantityValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nAn individual biochemical transformation carried out by a functional unit of an organism, in which a collection of substrates are transformed into a collection of products. Can also represent transporters
URI: nmdc:Reaction
classDiagram\n class Reaction\n FunctionalAnnotationTerm <|-- Reaction\n\n Reaction : alternative_identifiers\n\n Reaction : description\n\n Reaction : direction\n\n Reaction : id\n\n Reaction : is_balanced\n\n Reaction : is_diastereoselective\n\n Reaction : is_fully_characterized\n\n Reaction : is_stereo\n\n Reaction : is_transport\n\n Reaction : left_participants\n\n Reaction --|> ReactionParticipant : left_participants\n\n Reaction : name\n\n Reaction : right_participants\n\n Reaction --|> ReactionParticipant : right_participants\n\n Reaction : smarts_string\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG.REACTION
RHEA
MetaCyc
EC
GO
MetaNetX
SEED
RetroRules
name: Reaction\nid_prefixes:\n- KEGG.REACTION\n- RHEA\n- MetaCyc\n- EC\n- GO\n- MetaNetX\n- SEED\n- RetroRules\ndescription: An individual biochemical transformation carried out by a functional\n unit of an organism, in which a collection of substrates are transformed into a\n collection of products. Can also represent transporters\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:MolecularActivity\nis_a: FunctionalAnnotationTerm\nslots:\n- direction\n- is_balanced\n- is_diastereoselective\n- is_fully_characterized\n- is_stereo\n- is_transport\n- left_participants\n- right_participants\n- smarts_string\n\nname: Reaction\nid_prefixes:\n- KEGG.REACTION\n- RHEA\n- MetaCyc\n- EC\n- GO\n- MetaNetX\n- SEED\n- RetroRules\ndescription: An individual biochemical transformation carried out by a functional\n unit of an organism, in which a collection of substrates are transformed into a\n collection of products. Can also represent transporters\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:MolecularActivity\nis_a: FunctionalAnnotationTerm\nattributes:\n direction:\n name: direction\n description: One of l->r, r->l, bidirectional, neutral\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: direction\n owner: Reaction\n domain_of:\n - Reaction\n range: string\n is_balanced:\n name: is_balanced\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_balanced\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_diastereoselective:\n name: is_diastereoselective\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_diastereoselective\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_fully_characterized:\n name: is_fully_characterized\n description: False if includes R-groups\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_fully_characterized\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_stereo:\n name: is_stereo\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_stereo\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n is_transport:\n name: is_transport\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_transport\n owner: Reaction\n domain_of:\n - Reaction\n range: boolean\n left_participants:\n name: left_participants\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_participants\n multivalued: true\n alias: left_participants\n owner: Reaction\n domain_of:\n - Reaction\n range: ReactionParticipant\n right_participants:\n name: right_participants\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_participants\n multivalued: true\n alias: right_participants\n owner: Reaction\n domain_of:\n - Reaction\n range: ReactionParticipant\n smarts_string:\n name: smarts_string\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: smarts_string\n owner: Reaction\n domain_of:\n - Reaction\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Reaction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Reaction\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Reaction\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Reaction\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:ReactionActivity
classDiagram\n class ReactionActivity\n ReactionActivity : material_input\n\n ReactionActivity --|> MaterialSample : material_input\n\n ReactionActivity : material_output\n\n ReactionActivity --|> MaterialSample : material_output\n\n ReactionActivity : reaction_aided_by\n\n ReactionActivity --|> LabDevice : reaction_aided_by\n\n ReactionActivity : reaction_temperature\n\n ReactionActivity : reaction_time\n\n ReactionActivity --|> QuantityValue : reaction_time\n\n\nname: ReactionActivity\ntitle: Reaction activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reaction-activity\nslots:\n- material_input\n- material_output\n- reaction_aided_by\n- reaction_temperature\n- reaction_time\nslot_usage:\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n domain_of:\n - ReactionActivity\n\nname: ReactionActivity\ntitle: Reaction activity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reaction-activity\nslot_usage:\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n domain_of:\n - ReactionActivity\nattributes:\n material_input:\n name: material_input\n title: material input\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_input\n owner: ReactionActivity\n domain_of:\n - DissolvingActivity\n - ReactionActivity\n range: MaterialSample\n material_output:\n name: material_output\n title: material output\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: material_output\n owner: ReactionActivity\n domain_of:\n - DissolvingActivity\n - MaterialSamplingActivity\n - ReactionActivity\n range: MaterialSample\n reaction_aided_by:\n name: reaction_aided_by\n title: reaction aided by\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shaker\n rank: 1000\n alias: reaction_aided_by\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: LabDevice\n inlined: true\n reaction_temperature:\n name: reaction_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: reaction_temperature\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: string\n reaction_time:\n name: reaction_time\n todos:\n - constrain units\n - align with activity_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: reaction_time\n owner: ReactionActivity\n domain_of:\n - ReactionActivity\n range: QuantityValue\n inlined: true\n\nInstances of this link a reaction to a chemical entity participant
URI: nmdc:ReactionParticipant
classDiagram\n class ReactionParticipant\n ReactionParticipant : chemical\n\n ReactionParticipant --|> ChemicalEntity : chemical\n\n ReactionParticipant : stoichiometry\n\n\nname: ReactionParticipant\ndescription: Instances of this link a reaction to a chemical entity participant\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- chemical\n- stoichiometry\n\nname: ReactionParticipant\ndescription: Instances of this link a reaction to a chemical entity participant\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n chemical:\n name: chemical\n description: from reaction participant class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical\n owner: ReactionParticipant\n domain_of:\n - ReactionParticipant\n range: ChemicalEntity\n stoichiometry:\n name: stoichiometry\n description: from reaction participant class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stoichiometry\n owner: ReactionParticipant\n domain_of:\n - ReactionParticipant\n range: integer\n\nA workflow execution activity that performs taxonomy classification using sequencing reads
URI: nmdc:ReadBasedTaxonomyAnalysisActivity
classDiagram\n class ReadBasedTaxonomyAnalysisActivity\n WorkflowExecutionActivity <|-- ReadBasedTaxonomyAnalysisActivity\n\n ReadBasedTaxonomyAnalysisActivity : ended_at_time\n\n ReadBasedTaxonomyAnalysisActivity : execution_resource\n\n ReadBasedTaxonomyAnalysisActivity : git_url\n\n ReadBasedTaxonomyAnalysisActivity : has_input\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : has_input\n\n ReadBasedTaxonomyAnalysisActivity : has_output\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : has_output\n\n ReadBasedTaxonomyAnalysisActivity : id\n\n ReadBasedTaxonomyAnalysisActivity : name\n\n ReadBasedTaxonomyAnalysisActivity : part_of\n\n ReadBasedTaxonomyAnalysisActivity --|> NamedThing : part_of\n\n ReadBasedTaxonomyAnalysisActivity : started_at_time\n\n ReadBasedTaxonomyAnalysisActivity : type\n\n ReadBasedTaxonomyAnalysisActivity : used\n\n ReadBasedTaxonomyAnalysisActivity : version\n\n ReadBasedTaxonomyAnalysisActivity : was_informed_by\n\n ReadBasedTaxonomyAnalysisActivity --|> Activity : was_informed_by\n\n\nname: ReadBasedTaxonomyAnalysisActivity\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ReadBasedTaxonomyAnalysisActivity\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: ReadBasedTaxonomyAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nA workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
URI: nmdc:ReadQcAnalysisActivity
classDiagram\n class ReadQcAnalysisActivity\n WorkflowExecutionActivity <|-- ReadQcAnalysisActivity\n\n ReadQcAnalysisActivity : ended_at_time\n\n ReadQcAnalysisActivity : execution_resource\n\n ReadQcAnalysisActivity : git_url\n\n ReadQcAnalysisActivity : has_input\n\n ReadQcAnalysisActivity --|> NamedThing : has_input\n\n ReadQcAnalysisActivity : has_output\n\n ReadQcAnalysisActivity --|> NamedThing : has_output\n\n ReadQcAnalysisActivity : id\n\n ReadQcAnalysisActivity : input_base_count\n\n ReadQcAnalysisActivity : input_read_bases\n\n ReadQcAnalysisActivity : input_read_count\n\n ReadQcAnalysisActivity : name\n\n ReadQcAnalysisActivity : output_base_count\n\n ReadQcAnalysisActivity : output_read_bases\n\n ReadQcAnalysisActivity : output_read_count\n\n ReadQcAnalysisActivity : part_of\n\n ReadQcAnalysisActivity --|> NamedThing : part_of\n\n ReadQcAnalysisActivity : started_at_time\n\n ReadQcAnalysisActivity : type\n\n ReadQcAnalysisActivity : used\n\n ReadQcAnalysisActivity : version\n\n ReadQcAnalysisActivity : was_informed_by\n\n ReadQcAnalysisActivity --|> Activity : was_informed_by\n\n\nname: ReadQcAnalysisActivity\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslots:\n- type\n- input_read_count\n- input_base_count\n- output_read_count\n- output_base_count\n- input_read_bases\n- output_read_bases\n- version\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: ReadQcAnalysisActivity\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecutionActivity\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: ReadQcAnalysisActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n input_read_count:\n name: input_read_count\n description: The sequence count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_read_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n input_base_count:\n name: input_base_count\n description: The nucleotide base count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_base_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_read_count:\n name: output_read_count\n description: After QC analysis sequence count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_read_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_base_count:\n name: output_base_count\n description: After QC analysis nucleotide base count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_base_count\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n input_read_bases:\n name: input_read_bases\n description: 'TODO '\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_read_bases\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n output_read_bases:\n name: output_read_bases\n description: TODO\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: output_read_bases\n owner: ReadQcAnalysisActivity\n domain_of:\n - ReadQcAnalysisActivity\n range: float\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: ReadQcAnalysisActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: ReadQcAnalysisActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: ReadQcAnalysisActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: ReadQcAnalysisActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: ReadQcAnalysisActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadQcAnalysisActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: ReadQcAnalysisActivity\n domain_of:\n - Activity\n range: string\n\nURI: RelSampLocEnum
"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":"name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n edge of car:\n text: edge of car\n center of car:\n text: center of car\n under a seat:\n text: under a seat\n\nURI: RnaSampleFormatEnum
"},{"location":"RnaSampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RnaSampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RnaSampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RnaSampleFormatEnum/#schema-source","title":"Schema Source","text":"name: rna_sample_format_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: RoomCondtEnum
"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":"name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n visible signs of mold/mildew:\n text: visible signs of mold/mildew\n\nURI: RoomConnectedEnum
"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":"name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n office:\n text: office\n stairwell:\n text: stairwell\n\nURI: RoomLocEnum
"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":"name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n corner room:\n text: corner room\n interior room:\n text: interior room\n exterior wall:\n text: exterior wall\n\nURI: RoomSampPosEnum
"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":"name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north corner:\n text: north corner\n south corner:\n text: south corner\n west corner:\n text: west corner\n east corner:\n text: east corner\n northeast corner:\n text: northeast corner\n northwest corner:\n text: northwest corner\n southeast corner:\n text: southeast corner\n southwest corner:\n text: southwest corner\n center:\n text: center\n\nURI: RoomTypeEnum
"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":"name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n private office:\n text: private office\n open office:\n text: open office\n stairwell:\n text: stairwell\n ',restroom':\n text: ',restroom'\n lobby:\n text: lobby\n vestibule:\n text: vestibule\n mechanical or electrical room:\n text: mechanical or electrical room\n data center:\n text: data center\n laboratory_wet:\n text: laboratory_wet\n laboratory_dry:\n text: laboratory_dry\n gymnasium:\n text: gymnasium\n natatorium:\n text: natatorium\n auditorium:\n text: auditorium\n lockers:\n text: lockers\n cafe:\n text: cafe\n warehouse:\n text: warehouse\n\nURI: SampCaptStatusEnum
"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":"name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n active surveillance in response to an outbreak:\n text: active surveillance in response to an outbreak\n active surveillance not initiated by an outbreak:\n text: active surveillance not initiated by an outbreak\n farm sample:\n text: farm sample\n market sample:\n text: market sample\n other:\n text: other\n\nURI: SampCollectPointEnum
"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":"name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n well:\n text: well\n test well:\n text: test well\n drilling rig:\n text: drilling rig\n wellhead:\n text: wellhead\n separator:\n text: separator\n storage tank:\n text: storage tank\n other:\n text: other\n\nURI: SampDisStageEnum
"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":"name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dissemination:\n text: dissemination\n growth and reproduction:\n text: growth and reproduction\n infection:\n text: infection\n inoculation:\n text: inoculation\n penetration:\n text: penetration\n other:\n text: other\n\nURI: SampFloorEnum
"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":"name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 1st floor:\n text: 1st floor\n 2nd floor:\n text: 2nd floor\n basement:\n text: basement\n lobby:\n text: lobby\n\nURI: SampMdEnum
"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":"name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DF:\n text: DF\n RT:\n text: RT\n KB:\n text: KB\n MSL:\n text: MSL\n other:\n text: other\n\nURI: SampSubtypeEnum
"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":"name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n oil phase:\n text: oil phase\n water phase:\n text: water phase\n biofilm:\n text: biofilm\n not applicable:\n text: not applicable\n other:\n text: other\n\nURI: SampWeatherEnum
"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":"name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clear sky:\n text: clear sky\n cloudy:\n text: cloudy\n foggy:\n text: foggy\n hail:\n text: hail\n rain:\n text: rain\n snow:\n text: snow\n sleet:\n text: sleet\n sunny:\n text: sunny\n windy:\n text: windy\n\nSubset consisting of entities linked to the processing of samples. Currently, this subset consists of study, omics process, and biosample.
URI: SampleSubset
"},{"location":"SampleSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleSubset/#schema-source","title":"Schema Source","text":"Biological source material which can be characterized by an experiment.
"},{"location":"SampleSubset/#omicsprocessing","title":"OmicsProcessing","text":"The methods and processes used to generate omics data from a biosample or organism.
"},{"location":"SampleSubset/#study","title":"Study","text":"A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
"},{"location":"SampleTypeEnum/","title":"Enum: SampleTypeEnum","text":"URI: SampleTypeEnum
"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None water_extract_soil None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":"name: sample_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n soil:\n text: soil\n water_extract_soil:\n text: water_extract_soil\n\nURI: SamplingMethodEnum
"},{"location":"SamplingMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description weighing None"},{"location":"SamplingMethodEnum/#slots","title":"Slots","text":"Name Description sampling_method"},{"location":"SamplingMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplingMethodEnum/#schema-source","title":"Schema Source","text":"name: SamplingMethodEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n weighing:\n text: weighing\n title: Weighing\n\nURI: SeasonUseEnum
"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":"name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Spring:\n text: Spring\n Summer:\n text: Summer\n Fall:\n text: Fall\n Winter:\n text: Winter\n\nURI: SedimentTypeEnum
"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":"name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n biogenous:\n text: biogenous\n cosmogenous:\n text: cosmogenous\n hydrogenous:\n text: hydrogenous\n lithogenous:\n text: lithogenous\n\nURI: Sequencing
"},{"location":"Sequencing/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Sequencing/#schema-source","title":"Schema Source","text":"URI: ShadingDeviceCondEnum
"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":"name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: ShadingDeviceTypeEnum
"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bahama shutters:\n text: bahama shutters\n exterior roll blind:\n text: exterior roll blind\n gambrel awning:\n text: gambrel awning\n hood awning:\n text: hood awning\n porchroller awning:\n text: porchroller awning\n sarasota shutters:\n text: sarasota shutters\n slatted aluminum:\n text: slatted aluminum\n solid aluminum awning:\n text: solid aluminum awning\n sun screen:\n text: sun screen\n tree:\n text: tree\n trellis:\n text: trellis\n venetian awning:\n text: venetian awning\n\nURI: nmdc:Site
classDiagram\n class Site\n MaterialEntity <|-- Site\n\n\n Site <|-- FieldResearchSite\n\n\n Site : alternative_identifiers\n\n Site : description\n\n Site : id\n\n Site : name\n\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Site\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:site-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Site\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Site\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Site\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: SoilHorizonEnum
"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":"name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n O horizon:\n text: O horizon\n A horizon:\n text: A horizon\n E horizon:\n text: E horizon\n B horizon:\n text: B horizon\n C horizon:\n text: C horizon\n R layer:\n text: R layer\n Permafrost:\n text: Permafrost\n M horizon:\n text: M horizon\n\nURI: SolventEnum
"},{"location":"SolventEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description deionized_water None methanol CHEBI:17790 chloroform CHEBI:35255"},{"location":"SolventEnum/#slots","title":"Slots","text":"Name Description dissolution_reagent"},{"location":"SolventEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SolventEnum/#schema-source","title":"Schema Source","text":"name: SolventEnum\ntitle: Solvent enumeration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n deionized_water:\n text: deionized_water\n title: Deionized water\n broad_mappings:\n - CHEBI:15377\n methanol:\n text: methanol\n meaning: CHEBI:17790\n title: Methanol\n chloroform:\n text: chloroform\n meaning: CHEBI:35255\n title: Chloroform\n\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: SpecificEnum
"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":"name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n photos:\n text: photos\n\nURI: SrDepEnvEnum
"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":"name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Lacustine:\n text: Lacustine\n Fluvioldeltaic:\n text: Fluvioldeltaic\n Fluviomarine:\n text: Fluviomarine\n Marine:\n text: Marine\n other:\n text: other\n\nURI: SrGeolAgeEnum
"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: SrKerogTypeEnum
"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":"name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Type I:\n text: Type I\n Type II:\n text: Type II\n Type III:\n text: Type III\n Type IV:\n text: Type IV\n other:\n text: other\n\nURI: SrLithologyEnum
"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":"name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Clastic:\n text: Clastic\n Carbonate:\n text: Carbonate\n Coal:\n text: Coal\n Biosilicieous:\n text: Biosilicieous\n other:\n text: other\n\nURI: StatusEnum
"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description status"},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":"name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n pass:\n text: pass\n fail:\n text: fail\n\nA character string
URI: xsd:string
base: str
uri: xsd:string
A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
URI: nmdc:Study
classDiagram\n class Study\n NamedThing <|-- Study\n\n Study : alternative_descriptions\n\n Study : alternative_identifiers\n\n Study : alternative_names\n\n Study : alternative_titles\n\n Study : award_dois\n\n Study : dataset_dois\n\n Study : description\n\n Study : ecosystem\n\n Study : ecosystem_category\n\n Study : ecosystem_subtype\n\n Study : ecosystem_type\n\n Study : emsl_project_dois\n\n Study : ess_dive_datasets\n\n Study : funding_sources\n\n Study : gnps_task_identifiers\n\n Study : gold_study_identifiers\n\n Study : has_credit_associations\n\n Study --|> CreditAssociation : has_credit_associations\n\n Study : id\n\n Study : insdc_bioproject_identifiers\n\n Study : jgi_portal_study_identifiers\n\n Study : massive_study_identifiers\n\n Study : mgnify_project_identifiers\n\n Study : name\n\n Study : neon_study_identifiers\n\n Study : notes\n\n Study : objective\n\n Study : part_of\n\n Study --|> Study : part_of\n\n Study : principal_investigator\n\n Study --|> PersonValue : principal_investigator\n\n Study : publication_dois\n\n Study : publications\n\n Study : related_identifiers\n\n Study : relevant_protocols\n\n Study : specific_ecosystem\n\n Study : study_category\n\n Study --|> StudyCategoryEnum : study_category\n\n Study : study_image\n\n Study --|> ImageValue : study_image\n\n Study : title\n\n Study : type\n\n Study : websites\n\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research inititative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_dois\n- neon_study_identifiers\n- jgi_portal_study_identifiers\n- id\n- alternative_identifiers\n- gnps_task_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- description\n- award_dois\n- dataset_dois\n- publication_dois\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- ess_dive_datasets\n- funding_sources\n- gold_study_identifiers\n- has_credit_associations\n- study_category\n- insdc_bioproject_identifiers\n- massive_study_identifiers\n- mgnify_project_identifiers\n- notes\n- objective\n- part_of\n- principal_investigator\n- publications\n- related_identifiers\n- relevant_protocols\n- specific_ecosystem\n- study_image\n- title\n- type\n- websites\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n domain_of:\n - Study\n - PersonValue\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n domain_of:\n - Study\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n domain_of:\n - Study\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n domain_of:\n - Study\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n domain_of:\n - Study\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nin_subset:\n- sample subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research inititative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n domain_of:\n - Study\n - PersonValue\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n domain_of:\n - Study\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n domain_of:\n - Study\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n domain_of:\n - Study\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n domain_of:\n - Study\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\nattributes:\n emsl_project_dois:\n name: emsl_project_dois\n description: One or more DOIs that links to an EMSL Research Campaign page.\n title: EMSL Project DOI\n todos:\n - Make as a subproperty of award_dois\n examples:\n - value: doi:10.46936/intm.proj.2021.6014\n description: emsl_project_dois link to the document outlining the EMSL specific\n award for the project. Should not be used to link to datasets or publications.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n mixins:\n - emsl_identifiers\n multivalued: true\n alias: emsl_project_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n neon_study_identifiers:\n name: neon_study_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - neon_identifiers\n multivalued: true\n alias: neon_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n jgi_portal_study_identifiers:\n name: jgi_portal_study_identifiers\n id_prefixes:\n - jgi.proposal\n description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD\n API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n title: JGI Portal Study identifiers\n comments:\n - Could this could be considered a related identifier?\n - Curie suffix is the Site Award Number from an OSTI award page\n - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n study identifier gold:Gs0154044\n - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n examples:\n - value: jgi.proposal:507130\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - jgi_portal_identifiers\n multivalued: true\n alias: jgi_portal_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^jgi.proposal:\\d+$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: Study\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_identifiers\n owner: Study\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - MetaboliteQuantification\n range: uriorcurie\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n gnps_task_identifiers:\n name: gnps_task_identifiers\n description: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\n title: GNPS task identifiers\n comments:\n - this could be considered a related identifier, as the metabolomics progress\n and results aren't a study per se\n - this identifier was registered with bioregistry but not identifiers.org\n examples:\n - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gnps_identifiers\n multivalued: true\n alias: gnps_task_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^gnps\\.task:[a-f0-9]+$\n alternative_descriptions:\n name: alternative_descriptions\n description: A list of alternative descriptions for the entity. The distinction\n between description and alternative descriptions is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_descriptions\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_names:\n name: alternative_names\n annotations:\n display_hint:\n tag: display_hint\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: alternative_names\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_titles:\n name: alternative_titles\n description: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n rank: 1000\n multivalued: true\n alias: alternative_titles\n owner: Study\n domain_of:\n - Study\n range: string\n description:\n name: description\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Study\n domain_of:\n - Study\n - NamedThing\n - ImageValue\n range: string\n award_dois:\n name: award_dois\n description: One or more DOIs that links a study, or similar entiry, to information\n about the funding authority.\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: award_dois link to to an award document. Should not be used to\n link to datasets or publications. For example, doi:10.15485/1577267 is not\n an award doi, but a dataset doi.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: award_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n dataset_dois:\n name: dataset_dois\n description: One or more DOIs that links a study, or similar entity, to the generated\n data.\n examples:\n - value: doi:10.15485/1577267\n description: dataset_dois link to data encoded in a defined structure (as defined\n by DataCite). Should not be used to link to publications or administrative\n information like funding requests or awards.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: dataset_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n publication_dois:\n name: publication_dois\n description: One or more DOIs that links a study, or similar entity, to a publication.\n examples:\n - value: doi:10.1126/science.1058040\n description: publication_dois link to a prose document, preferably a peer-reviewed\n journal article. Should not be used to link to datasets or administrative\n information like funding requests or awards\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: dois\n multivalued: true\n alias: publication_dois\n owner: Study\n domain_of:\n - Study\n range: uriorcurie\n pattern: ^doi:10.\\d{2,9}/.*$\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ess_dive_datasets:\n name: ess_dive_datasets\n description: List of ESS-DIVE dataset DOIs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: ess_dive_datasets\n owner: Study\n domain_of:\n - Study\n range: string\n funding_sources:\n name: funding_sources\n description: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process\n applications and award funds to the chosen qualified applicants.\n comments:\n - Include only the name of the funding organization and the award or contract\n number.\n examples:\n - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n - value: U.S. Department of Energy, Office of Science, Office of Biological and\n Environmental Research (BER) under contract DE-AC05-00OR2275\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C39409\n rank: 1000\n multivalued: true\n alias: funding_sources\n owner: Study\n domain_of:\n - Study\n range: string\n gold_study_identifiers:\n name: gold_study_identifiers\n description: identifiers for corresponding project(s) in GOLD\n title: GOLD Study Identifiers\n comments:\n - uses the prefix GS (but possibly in a different case)\n examples:\n - value: https://bioregistry.io/gold:Gs0110115\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/studies\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gold_identifiers\n multivalued: true\n alias: gold_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^gold:Gs[0-9]+$\n has_credit_associations:\n name: has_credit_associations\n annotations:\n display_hint:\n tag: display_hint\n value: Other researchers associated with this study.\n description: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\n notes:\n - 'had just been \"inlined: true\"'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Study\n slot_uri: prov:qualifiedAssociation\n multivalued: true\n alias: has_credit_associations\n owner: Study\n domain_of:\n - Study\n range: CreditAssociation\n inlined: true\n inlined_as_list: true\n study_category:\n name: study_category\n description: The type of research initiative\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_category\n owner: Study\n domain_of:\n - Study\n range: StudyCategoryEnum\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n display_hint:\n tag: display_hint\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n multivalued: true\n alias: insdc_bioproject_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n massive_study_identifiers:\n name: massive_study_identifiers\n description: identifiers for corresponding study in MASSIVE\n todos:\n - prefix not defined yet\n examples:\n - value: MASSIVE:MSV000090886\n description: MASSIVE id for MASSIVE's metabolomics analysis of Gb0305843, resolvable\n with prefix http://identifiers.org/massive/\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=83574f41458a4b259621d5c32a4d82f9\n rank: 1000\n is_a: study_identifiers\n mixins:\n - massive_identifiers\n multivalued: true\n alias: massive_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: '^MASSIVE:'\n mgnify_project_identifiers:\n name: mgnify_project_identifiers\n description: identifiers for corresponding project in MGnify\n examples:\n - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - mgnify_identifiers\n multivalued: true\n alias: mgnify_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n notes:\n name: notes\n annotations:\n display_hint:\n tag: display_hint\n value: Add any additional notes or comments about this study.\n description: from study class\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: notes\n owner: Study\n domain_of:\n - Study\n range: string\n objective:\n name: objective\n description: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - SIO:000337\n rank: 1000\n multivalued: false\n alias: objective\n owner: Study\n domain_of:\n - Study\n range: string\n part_of:\n name: part_of\n description: Links a study or consortium to a parent study or consortium.\n comments:\n - Value is the id of the parent study or consortium.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: Study\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: Study\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n is_a: attribute\n alias: principal_investigator\n owner: Study\n domain_of:\n - Study\n - OmicsProcessing\n range: PersonValue\n publications:\n name: publications\n description: A list of publications that are associated with the entity. The publications\n SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: publications\n owner: Study\n domain_of:\n - Study\n range: string\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n title: Related Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: related_identifiers\n owner: Study\n domain_of:\n - Study\n range: string\n relevant_protocols:\n name: relevant_protocols\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: relevant_protocols\n owner: Study\n domain_of:\n - Study\n range: string\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n study_image:\n name: study_image\n description: Links a study to one or more images.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: Study\n multivalued: true\n alias: study_image\n owner: Study\n domain_of:\n - Study\n range: ImageValue\n inlined: true\n title:\n name: title\n description: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the\n GOLD system has assigned a name/label. However, for display purposes, we may\n also wish the capture the title of the proposal that was used to fund the study.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:title\n rank: 1000\n alias: title\n owner: Study\n domain_of:\n - Study\n range: string\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: Study\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n websites:\n name: websites\n annotations:\n display_hint:\n tag: display_hint\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n description: A list of websites that are associated with the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n multivalued: true\n alias: websites\n owner: Study\n domain_of:\n - Study\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n display_hint:\n tag: display_hint\n value: Provide a name for the study your samples will belong with.\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Study\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n\nURI: StudyCategoryEnum
"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":"name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n research_study:\n text: research_study\n description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n experiment.\n exact_mappings:\n - SIO:001066\n - NCIT:C63536\n - ISA:Study\n close_mappings:\n - OBI:0000355\n consortium:\n text: consortium\n description: A group formed to undertake a venture that is beyond the capabilities\n of the individual members. Each member of the consortium brings a high level\n of expertise in a specific area to ensure the successful completion of the project.\n comments:\n - A consortium has collections of data, those data do not come from a hypothesis-driven\n experiment.\n exact_mappings:\n - NCIT:C61538\n\nURI: SubstructureTypeEnum
"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":"name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crawlspace:\n text: crawlspace\n slab on grade:\n text: slab on grade\n basement:\n text: basement\n\nURI: SurfAirContEnum
"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":"name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dust:\n text: dust\n organic matter:\n text: organic matter\n particulate matter:\n text: particulate matter\n volatile organic compounds:\n text: volatile organic compounds\n biological contaminants:\n text: biological contaminants\n radon:\n text: radon\n nutrients:\n text: nutrients\n biocides:\n text: biocides\n\nURI: SurfMaterialEnum
"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":"name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n adobe:\n text: adobe\n carpet:\n text: carpet\n cinder blocks:\n text: cinder blocks\n concrete:\n text: concrete\n hay bales:\n text: hay bales\n glass:\n text: glass\n metal:\n text: metal\n paint:\n text: paint\n plastic:\n text: plastic\n stainless steel:\n text: stainless steel\n stone:\n text: stone\n stucco:\n text: stucco\n tile:\n text: tile\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nA basic string value
URI: nmdc:TextValue
classDiagram\n class TextValue\n AttributeValue <|-- TextValue\n\n TextValue : has_raw_value\n\n TextValue : language\n\n TextValue : was_generated_by\n\n TextValue --|> Activity : was_generated_by\n\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n language:\n name: language\n description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: language\n owner: TextValue\n domain_of:\n - TextValue\n range: language code\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: TextValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: TextValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: TidalStageEnum
"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":"name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low tide:\n text: low tide\n ebb tide:\n text: ebb tide\n flood tide:\n text: flood tide\n high tide:\n text: high tide\n\nURI: TillageEnum
"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":"name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drill:\n text: drill\n cutting disc:\n text: cutting disc\n ridge till:\n text: ridge till\n strip tillage:\n text: strip tillage\n zonal tillage:\n text: zonal tillage\n chisel:\n text: chisel\n tined:\n text: tined\n mouldboard:\n text: mouldboard\n disc plough:\n text: disc plough\n\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
A value that is a timestamp. The range should be ISO-8601
URI: nmdc:TimestampValue
classDiagram\n class TimestampValue\n AttributeValue <|-- TimestampValue\n\n TimestampValue : has_raw_value\n\n TimestampValue : was_generated_by\n\n TimestampValue --|> Activity : was_generated_by\n\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: TimestampValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: TimestampValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: TrainLineEnum
"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":"name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n red:\n text: red\n green:\n text: green\n orange:\n text: orange\n\nURI: TrainStatLocEnum
"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":"name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n south station above ground:\n text: south station above ground\n south station underground:\n text: south station underground\n south station amtrak:\n text: south station amtrak\n forest hills:\n text: forest hills\n riverside:\n text: riverside\n\nURI: TrainStopLocEnum
"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":"name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n end:\n text: end\n mid:\n text: mid\n downtown:\n text: downtown\n\nURI: xsd:string
base: str
uri: xsd:string
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
A value that is a string that conforms to URL syntax
URI: nmdc:UrlValue
classDiagram\n class UrlValue\n AttributeValue <|-- UrlValue\n\n UrlValue : has_raw_value\n\n UrlValue : was_generated_by\n\n UrlValue --|> Activity : was_generated_by\n\n\nname: UrlValue\ndescription: A value that is a string that conforms to URL syntax\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\n\nname: UrlValue\ndescription: A value that is a string that conforms to URL syntax\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: AttributeValue\n multivalued: false\n alias: has_raw_value\n owner: UrlValue\n domain_of:\n - AttributeValue\n - QuantityValue\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: UrlValue\n domain_of:\n - DataObject\n - AttributeValue\n - FunctionalAnnotation\n range: Activity\n\nURI: VisMediaEnum
"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":"name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n photos:\n text: photos\n videos:\n text: videos\n commonly of the building:\n text: commonly of the building\n site context (adjacent buildings, vegetation, terrain, streets):\n text: site context (adjacent buildings, vegetation, terrain, streets)\n interiors:\n text: interiors\n equipment:\n text: equipment\n 3D scans:\n text: 3D scans\n\nURI: WallConstTypeEnum
"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":"name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n frame construction:\n text: frame construction\n joisted masonry:\n text: joisted masonry\n light noncombustible:\n text: light noncombustible\n masonry noncombustible:\n text: masonry noncombustible\n modified fire resistive:\n text: modified fire resistive\n fire resistive:\n text: fire resistive\n\nURI: WallFinishMatEnum
"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":"name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plaster:\n text: plaster\n gypsum plaster:\n text: gypsum plaster\n veneer plaster:\n text: veneer plaster\n gypsum board:\n text: gypsum board\n tile:\n text: tile\n terrazzo:\n text: terrazzo\n stone facing:\n text: stone facing\n acoustical treatment:\n text: acoustical treatment\n wood:\n text: wood\n metal:\n text: metal\n masonry:\n text: masonry\n\nURI: WallLocEnum
"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":"name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WallSurfTreatmentEnum
"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":"name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n painted:\n text: painted\n wall paper:\n text: wall paper\n no treatment:\n text: no treatment\n paneling:\n text: paneling\n stucco:\n text: stucco\n fabric:\n text: fabric\n\nURI: WallTextureEnum
"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":"name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n ? ''\n : text: ''\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: WaterFeatTypeEnum
"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":"name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fountain:\n text: fountain\n pool:\n text: pool\n standing feature:\n text: standing feature\n stream:\n text: stream\n waterfall:\n text: waterfall\n\nURI: WeekdayEnum
"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":"name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Monday:\n text: Monday\n Tuesday:\n text: Tuesday\n Wednesday:\n text: Wednesday\n Thursday:\n text: Thursday\n Friday:\n text: Friday\n Saturday:\n text: Saturday\n Sunday:\n text: Sunday\n\nURI: WindowCondEnum
"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":"name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: WindowCoverEnum
"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":"name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n blinds:\n text: blinds\n curtains:\n text: curtains\n none:\n text: none\n\nURI: WindowHorizPosEnum
"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":"name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n left:\n text: left\n middle:\n text: middle\n right:\n text: right\n\nURI: WindowLocEnum
"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":"name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WindowMatEnum
"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":"name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clad:\n text: clad\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: WindowTypeEnum
"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":"name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n single-hung sash window:\n text: single-hung sash window\n horizontal sash window:\n text: horizontal sash window\n fixed window:\n text: fixed window\n\nURI: WindowVertPosEnum
"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":"name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bottom:\n text: bottom\n middle:\n text: middle\n top:\n text: top\n low:\n text: low\n high:\n text: high\n\nRepresents an instance of an execution of a particular workflow
URI: nmdc:WorkflowExecutionActivity
classDiagram\n class WorkflowExecutionActivity\n Activity <|-- WorkflowExecutionActivity\n\n\n WorkflowExecutionActivity <|-- MetagenomeAssembly\n WorkflowExecutionActivity <|-- MetatranscriptomeAssembly\n WorkflowExecutionActivity <|-- MetagenomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeAnnotationActivity\n WorkflowExecutionActivity <|-- MetatranscriptomeActivity\n WorkflowExecutionActivity <|-- MagsAnalysisActivity\n WorkflowExecutionActivity <|-- MetagenomeSequencingActivity\n WorkflowExecutionActivity <|-- ReadQcAnalysisActivity\n WorkflowExecutionActivity <|-- ReadBasedTaxonomyAnalysisActivity\n WorkflowExecutionActivity <|-- MetabolomicsAnalysisActivity\n WorkflowExecutionActivity <|-- MetaproteomicsAnalysisActivity\n WorkflowExecutionActivity <|-- NomAnalysisActivity\n\n\n WorkflowExecutionActivity : ended_at_time\n\n WorkflowExecutionActivity : execution_resource\n\n WorkflowExecutionActivity : git_url\n\n WorkflowExecutionActivity : has_input\n\n WorkflowExecutionActivity --|> NamedThing : has_input\n\n WorkflowExecutionActivity : has_output\n\n WorkflowExecutionActivity --|> NamedThing : has_output\n\n WorkflowExecutionActivity : id\n\n WorkflowExecutionActivity : name\n\n WorkflowExecutionActivity : part_of\n\n WorkflowExecutionActivity --|> NamedThing : part_of\n\n WorkflowExecutionActivity : started_at_time\n\n WorkflowExecutionActivity : type\n\n WorkflowExecutionActivity : used\n\n WorkflowExecutionActivity : version\n\n WorkflowExecutionActivity : was_informed_by\n\n WorkflowExecutionActivity --|> Activity : was_informed_by\n\n\nname: WorkflowExecutionActivity\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) activities is a distinct run with start and\n stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: Activity\nslots:\n- execution_resource\n- git_url\n- has_input\n- has_output\n- part_of\n- type\n- version\nslot_usage:\n started_at_time:\n name: started_at_time\n domain_of:\n - Activity\n required: true\n ended_at_time:\n name: ended_at_time\n domain_of:\n - Activity\n required: true\n git_url:\n name: git_url\n domain_of:\n - WorkflowExecutionActivity\n required: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n execution_resource:\n name: execution_resource\n domain_of:\n - WorkflowExecutionActivity\n required: true\n type:\n name: type\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n\nname: WorkflowExecutionActivity\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) activities is a distinct run with start and\n stop times, potentially with different inputs and outputs\nin_subset:\n- workflow subset\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: Activity\nslot_usage:\n started_at_time:\n name: started_at_time\n domain_of:\n - Activity\n required: true\n ended_at_time:\n name: ended_at_time\n domain_of:\n - Activity\n required: true\n git_url:\n name: git_url\n domain_of:\n - WorkflowExecutionActivity\n required: true\n has_input:\n name: has_input\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n has_output:\n name: has_output\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n required: true\n execution_resource:\n name: execution_resource\n domain_of:\n - WorkflowExecutionActivity\n required: true\n type:\n name: type\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n required: true\n id:\n name: id\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\nattributes:\n execution_resource:\n name: execution_resource\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: execution_resource\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n git_url:\n name: git_url\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: attribute\n alias: git_url\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n range: string\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_input\n owner: WorkflowExecutionActivity\n domain_of:\n - BiosampleProcessing\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n has_output:\n name: has_output\n description: An output biosample to a processing step\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n domain: NamedThing\n multivalued: true\n alias: has_output\n owner: WorkflowExecutionActivity\n domain_of:\n - OmicsProcessing\n - WorkflowExecutionActivity\n - PlannedProcess\n range: NamedThing\n required: true\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n domain: NamedThing\n slot_uri: dcterms:isPartOf\n multivalued: true\n alias: part_of\n owner: WorkflowExecutionActivity\n domain_of:\n - FieldResearchSite\n - Biosample\n - Study\n - OmicsProcessing\n - WorkflowExecutionActivity\n range: NamedThing\n type:\n name: type\n description: An optional string that specifies the type object. This is used\n to allow for searches for different kinds of objects.\n deprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: type\n owner: WorkflowExecutionActivity\n domain_of:\n - DataObject\n - Biosample\n - Study\n - OmicsProcessing\n - CreditAssociation\n - WorkflowExecutionActivity\n - MetagenomeAssembly\n - MetagenomeAnnotationActivity\n - MetatranscriptomeAnnotationActivity\n - MetatranscriptomeActivity\n - MagsAnalysisActivity\n - ReadQcAnalysisActivity\n - ReadBasedTaxonomyAnalysisActivity\n - MagBin\n - GenomeFeature\n range: string\n required: true\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: WorkflowExecutionActivity\n domain_of:\n - WorkflowExecutionActivity\n - ReadQcAnalysisActivity\n range: string\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n identifier: true\n alias: id\n owner: WorkflowExecutionActivity\n domain_of:\n - Biosample\n - Study\n - NamedThing\n - Activity\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wf-{id_shoulder}-{id_blade}{id_version}{id_locus}'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: WorkflowExecutionActivity\n domain_of:\n - Protocol\n - QualityControlReport\n - NamedThing\n - PersonValue\n - Activity\n range: string\n started_at_time:\n name: started_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: started_at_time\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n ended_at_time:\n name: ended_at_time\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ended_at_time\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: Activity\n used:\n name: used\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:used\n rank: 1000\n domain: Activity\n alias: used\n owner: WorkflowExecutionActivity\n domain_of:\n - Activity\n range: string\n\nSubset consisting of just the workflow execution activities
URI: WorkflowSubset
"},{"location":"WorkflowSubset/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WorkflowSubset/#schema-source","title":"Schema Source","text":"A workflow execution activity that uses computational binning tools to group assembled contigs into genomes
"},{"location":"WorkflowSubset/#metabolomicsanalysisactivity","title":"MetabolomicsAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#metagenomeannotationactivity","title":"MetagenomeAnnotationActivity","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
"},{"location":"WorkflowSubset/#metagenomeassembly","title":"MetagenomeAssembly","text":"A workflow execution activity that converts sequencing reads into an assembled metagenome.
"},{"location":"WorkflowSubset/#metagenomesequencingactivity","title":"MetagenomeSequencingActivity","text":"Initial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
"},{"location":"WorkflowSubset/#metaproteomicsanalysisactivity","title":"MetaproteomicsAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#metatranscriptomeactivity","title":"MetatranscriptomeActivity","text":"A metatranscriptome activity that e.g. pools assembly and annotation activity.
"},{"location":"WorkflowSubset/#metatranscriptomeannotationactivity","title":"MetatranscriptomeAnnotationActivity","text":"None
"},{"location":"WorkflowSubset/#metatranscriptomeassembly","title":"MetatranscriptomeAssembly","text":"None
"},{"location":"WorkflowSubset/#nomanalysisactivity","title":"NomAnalysisActivity","text":"None
"},{"location":"WorkflowSubset/#readbasedtaxonomyanalysisactivity","title":"ReadBasedTaxonomyAnalysisActivity","text":"A workflow execution activity that performs taxonomy classification using sequencing reads
"},{"location":"WorkflowSubset/#readqcanalysisactivity","title":"ReadQcAnalysisActivity","text":"A workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
"},{"location":"WorkflowSubset/#workflowexecutionactivity","title":"WorkflowExecutionActivity","text":"Represents an instance of an execution of a particular workflow
"},{"location":"YesNoEnum/","title":"Enum: YesNoEnum","text":"replaces DnaDnaseEnum and DnaseRnaEnum
URI: YesNoEnum
"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dnase_rna dna_dnase"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":"name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 'no':\n text: 'no'\n 'yes':\n text: 'yes'\n\nSchema resources for the National Microbiome Data Collaborative (NMDC)
"},{"location":"abs_air_humidity/","title":"Slot: abs_air_humidity","text":"Actual mass of water vapor - mh20 - present in the air water vapor mixture
URI: MIXS:0000122
"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":"name: abs_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nmultivalued: false\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of workflow activities.
URI: nmdc:activity_set
"},{"location":"activity_set/#inheritance","title":"Inheritance","text":"Range: WorkflowExecutionActivity
Multivalued: True
name: activity_set\ndescription: This property links a database object to the set of workflow activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: activity_set\ndomain_of:\n- Database\nrange: WorkflowExecutionActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:activity_speed
"},{"location":"activity_speed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_speed/#properties","title":"Properties","text":"name: activity_speed\ntitle: activity speed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shake_speed\nrank: 1000\nalias: activity_speed\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:activity_temperature
"},{"location":"activity_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_temperature/#properties","title":"Properties","text":"name: activity_temperature\ntodos:\n- constrain units\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: activity_temperature\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:activity_time
"},{"location":"activity_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"activity_time/#properties","title":"Properties","text":"name: activity_time\ntitle: activity time\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shake_time\nrank: 1000\nalias: activity_time\ndomain_of:\n- LabDevice\nrange: QuantityValue\ninlined: true\n\nThe date on which the information was added to the database.
URI: nmdc:add_date
"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"add_date/#properties","title":"Properties","text":"name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: string\n\nAdditional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001009
"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":"name: add_recov_method\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one of\n them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nmultivalued: false\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
URI: MIXS:0000300
"},{"location":"additional_info/#inheritance","title":"Inheritance","text":"name: additional_info\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nmultivalued: false\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe street name and building number where the sampling occurred.
URI: MIXS:0000218
"},{"location":"address/#inheritance","title":"Inheritance","text":"name: address\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nmultivalued: false\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of rooms (room number, room name) immediately adjacent to the sampling room
URI: MIXS:0000219
"},{"location":"adj_room/#inheritance","title":"Inheritance","text":"name: adj_room\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nmultivalued: false\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\n\nAerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
URI: MIXS:0000773
"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":"name: aero_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nmultivalued: false\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\n\nAddition of fertilizers, pesticides, etc. - amount and time of applications
URI: MIXS:0000639
"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: agrochem_addition\nannotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nmultivalued: true\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
URI: MIXS:0000108
"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_PM_concen\nannotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nmultivalued: true\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\n\nTemperature of the air at the time of sampling
URI: MIXS:0000124
"},{"location":"air_temp/#inheritance","title":"Inheritance","text":"name: air_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nmultivalued: false\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens
URI: MIXS:0000551
"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nmultivalued: true\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAluminum saturation (esp. For tropical soils)
URI: MIXS:0000607
"},{"location":"al_sat/#inheritance","title":"Inheritance","text":"name: al_sat\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nmultivalued: false\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining Al saturation
URI: MIXS:0000324
"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":"name: al_sat_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nmultivalued: false\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nAlkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
URI: MIXS:0000421
"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":"name: alkalinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nmultivalued: false\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod used for alkalinity measurement
URI: MIXS:0000298
"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":"name: alkalinity_method\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nmultivalued: false\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of alkyl diethers
URI: MIXS:0000490
"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":"name: alkyl_diethers\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nmultivalued: false\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nthe list of protein identifiers that are associated with the peptide sequence
URI: nmdc:all_proteins
"},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"all_proteins/#properties","title":"Properties","text":"Range: GeneProduct
Multivalued: True
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nAltitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air
URI: MIXS:0000094
"},{"location":"alt/#inheritance","title":"Inheritance","text":"name: alt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n layers and clouds. It is used to measure the height of an object which is above\n the earth's surface. In this context, the altitude measurement is the vertical distance\n between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nmultivalued: false\nalias: alt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOne or more other email addresses for an entity.
URI: nmdc:alternate_emails
"},{"location":"alternate_emails/#properties","title":"Properties","text":"name: alternate_emails\ndescription: One or more other email addresses for an entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternate_emails\nrange: string\n\nA list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.
URI: nmdc:alternative_descriptions
"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\n\nA list of alternative identifiers for the entity.
URI: nmdc:alternative_identifiers
"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: alternative_identifiers\ndomain_of:\n- Biosample\n- Study\n- NamedThing\n- MetaboliteQuantification\nrange: uriorcurie\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nA list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.
URI: nmdc:alternative_names
"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"alternative_names/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nmultivalued: true\nalias: alternative_names\ndomain_of:\n- Study\nrange: string\n\nA list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.
URI: nmdc:alternative_titles
"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nmultivalued: true\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\n\nMeasurement of aminopeptidase activity
URI: MIXS:0000172
"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":"name: aminopept_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nmultivalued: false\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of ammonium in the sample
URI: MIXS:0000427
"},{"location":"ammonium/#inheritance","title":"Inheritance","text":"name: ammonium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nmultivalued: false\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of ammonium nitrogen in the sample
URI: nmdc:ammonium_nitrogen
"},{"location":"ammonium_nitrogen/#inheritance","title":"Inheritance","text":"name: ammonium_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nis_a: attribute\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:amount_collected
"},{"location":"amount_collected/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity yes"},{"location":"amount_collected/#properties","title":"Properties","text":"name: amount_collected\ntitle: amount collected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: amount_collected\ndomain_of:\n- MaterialSamplingActivity\nrange: QuantityValue\ninlined: true\n\nThe unit of illuminance and luminous emittance, measuring luminous flux per unit area
URI: MIXS:0000140
"},{"location":"amount_light/#inheritance","title":"Inheritance","text":"name: amount_light\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nmultivalued: false\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:analysis_identifiers
"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: analysis_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSelect all the data types associated or available for this biosample
URI: nmdc:analysis_type
"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":"Range: AnalysisTypeEnum
Multivalued: True
Recommended: True
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; proteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nmultivalued: true\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: analysis_type_enum\nrecommended: true\n\nInformation about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)
URI: MIXS:0000247
"},{"location":"ances_data/#inheritance","title":"Inheritance","text":"name: ances_data\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about either pedigree or other ancestral information description\n (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nmultivalued: false\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000644
"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":"name: annual_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nmultivalued: false\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMean annual temperature
URI: MIXS:0000642
"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":"name: annual_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nmultivalued: false\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens
URI: MIXS:0000553
"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: antibiotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving antibiotic administration; should\n include the name of antibiotic, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nmultivalued: true\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAPI gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)
URI: MIXS:0000157
"},{"location":"api/#inheritance","title":"Inheritance","text":"name: api\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nmultivalued: false\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: prov:hadRole
"},{"location":"applied_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_role/#properties","title":"Properties","text":"name: applied_role\ndeprecated: A credit association may have multiple roles. So, use the applied roles\n slot.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nslot_uri: prov:hadRole\nalias: applied_role\ndomain_of:\n- CreditAssociation\nrange: credit enum\n\nURI: nmdc:applied_roles
"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":"Range: CreditEnum
Multivalued: True
Required: True
name: applied_roles\nannotations:\n display_hint:\n tag: display_hint\n value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nmultivalued: true\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: credit enum\nrequired: true\n\nURI: nmdc:applies_to_person
"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":"Range: PersonValue
Required: True
name: applies_to_person\ntodos:\n- prov:agent takes an Agent object. Is a person value an Agent? Also try to relate\n to principal investigator slot? could include OBI:0000103 principal investigator\n role... do we need to define the OBI prefix?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: CreditAssociation\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\nAn architectural structure is a human-made, free-standing, immobile outdoor construction
URI: MIXS:0000774
"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":"name: arch_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nmultivalued: false\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000133
"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":"name: aromatics_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nmultivalued: false\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nA score for comparing metagenomic assembly quality from same sample.
URI: nmdc:asm_score
"},{"location":"asm_score/#inheritance","title":"Inheritance","text":"name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000135
"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":"name: asphaltenes_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nmultivalued: false\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:assembly_identifiers
"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":"name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\nMeasurement of atmospheric data; can include multiple data
URI: MIXS:0001097
"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: atmospheric_data\nannotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nmultivalued: true\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\n\nA attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template
URI: nmdc:attribute
"},{"location":"attribute/#inheritance","title":"Inheritance","text":"name: attribute\ndescription: 'A attribute of a biosample. Examples: depth, habitat, material. For\n NMDC, attributes SHOULD be mapped to terms within a MIxS template'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field\n- property\n- template field\n- key\n- characteristic\nrank: 1000\nabstract: true\nalias: attribute\nrange: string\n\nThe average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000141
"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":"name: avg_dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nmultivalued: false\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDaily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.
URI: MIXS:0000775
"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":"name: avg_occup\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nmultivalued: false\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000142
"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":"name: avg_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nmultivalued: false\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOne or more DOIs that links a study, or similar entiry, to information about the funding authority.
URI: nmdc:award_dois
"},{"location":"award_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: award_dois\ndescription: One or more DOIs that links a study, or similar entiry, to information\n about the funding authority.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n description: award_dois link to to an award document. Should not be used to link\n to datasets or publications. For example, doi:10.15485/1577267 is not an award\n doi, but a dataset doi.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: award_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nBacterial production in the water column measured by isotope uptake
URI: MIXS:0000683
"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":"name: bac_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nmultivalued: false\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of bacterial respiration in the water column
URI: MIXS:0000684
"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":"name: bac_resp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nmultivalued: false\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of bacterial carbon production
URI: MIXS:0000173
"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":"name: bacteria_carb_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nmultivalued: false\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nForce per unit area exerted against a surface by the weight of air above that surface
URI: MIXS:0000096
"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":"name: barometric_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nmultivalued: false\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nName of the basin (e.g. Campos)
URI: MIXS:0000290
"},{"location":"basin/#inheritance","title":"Inheritance","text":"name: basin\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nmultivalued: false\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe number of bathrooms in the building
URI: MIXS:0000776
"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":"name: bathroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nmultivalued: false\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe number of bedrooms in the building
URI: MIXS:0000777
"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":"name: bedroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nmultivalued: false\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of benzene in the sample
URI: MIXS:0000153
"},{"location":"benzene/#inheritance","title":"Inheritance","text":"name: benzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nmultivalued: false\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nthe specific protein identifier most correctly associated with the peptide sequence
URI: nmdc:best_protein
"},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein yes"},{"location":"best_protein/#properties","title":"Properties","text":"name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nURI: nmdc:bin_name
"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":"name: bin_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:bin_quality
"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":"name: bin_quality\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:binned_contig_num
"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":"name: binned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nAmount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
URI: MIXS:0000653
"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: biochem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n a body of water to break down organic material present in a given water sample at\n certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nmultivalued: false\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nList of biocides (commercial name of product and supplier) and date of administration
URI: MIXS:0001011
"},{"location":"biocide/#inheritance","title":"Inheritance","text":"name: biocide\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nmultivalued: false\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\n\nMethod of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
URI: MIXS:0000456
"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":"name: biocide_admin_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nmultivalued: false\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:biogas_retention_time
"},{"location":"biogas_retention_time/#properties","title":"Properties","text":"name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\nURI: nmdc:biogas_temperature
"},{"location":"biogas_temperature/#properties","title":"Properties","text":"name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\nThe level of genome modification.
URI: MIXS:0000858
"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":"name: biol_stat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nmultivalued: false\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\n\nAmount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
URI: MIXS:0000174
"},{"location":"biomass/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: biomass\nannotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nmultivalued: true\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:biomaterial_purity
"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":"name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\nURI: nmdc:biosample_categories
"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":"Range: BiosampleCategoryEnum
Multivalued: True
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\n\nURI: nmdc:biosample_identifiers
"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: biosample_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of samples within it.
URI: nmdc:biosample_set
"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":"Range: Biosample
Multivalued: True
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\ninlined: true\ninlined_as_list: true\n\nInformation about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.
URI: MIXS:0001038
"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":"name: biotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nmultivalued: false\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nDescription of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
URI: MIXS:0000028
"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":"name: biotic_relationship\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n Y. The target organism is the subject of the relationship, and the other organism(s)\n is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nmultivalued: false\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\n\nConcentration of bishomohopanol
URI: MIXS:0000175
"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":"name: bishomohopanol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nmultivalued: false\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nResting diastolic blood pressure, measured as mm mercury
URI: MIXS:0000258
"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":"name: blood_press_diast\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nmultivalued: false\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nResting systolic blood pressure, measured as mm mercury
URI: MIXS:0000259
"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":"name: blood_press_syst\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nmultivalued: false\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of bromide
URI: MIXS:0000176
"},{"location":"bromide/#inheritance","title":"Inheritance","text":"name: bromide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nmultivalued: false\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building design, construction and operation documents
URI: MIXS:0000787
"},{"location":"build_docs/#inheritance","title":"Inheritance","text":"name: build_docs\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nmultivalued: false\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\n\nThe primary function for which a building or discrete part of a building is intended to be used
URI: MIXS:0000761
"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":"Range: BuildOccupTypeEnum
Multivalued: True
name: build_occup_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The primary function for which a building or discrete part of a building\n is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nmultivalued: true\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\n\nA location (geography) where a building is set
URI: MIXS:0000768
"},{"location":"building_setting/#inheritance","title":"Inheritance","text":"name: building_setting\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nmultivalued: false\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\n\nThe age of the built structure since construction
URI: MIXS:0000145
"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":"name: built_struc_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nmultivalued: false\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe characterization of the location of the built structure as high or low human density
URI: MIXS:0000778
"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":"name: built_struc_set\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The characterization of the location of the built structure as high or\n low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nmultivalued: false\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\n\nA physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
URI: MIXS:0000721
"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":"name: built_struc_type\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nmultivalued: false\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of calcium in the sample
URI: MIXS:0000432
"},{"location":"calcium/#inheritance","title":"Inheritance","text":"name: calcium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nmultivalued: false\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\na slot that can be added and removed as evidence that schema changes have propagated to other systems
URI: nmdc:canary
"},{"location":"canary/#properties","title":"Properties","text":"name: canary\ndescription: a slot that can be added and removed as evidence that schema changes\n have propagated to other systems\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: canary\nrange: string\n\nCarbon dioxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000097
"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":"name: carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nmultivalued: false\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCarbon monoxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000098
"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":"name: carb_monoxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nmultivalued: false\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nRatio of amount or concentrations of carbon to nitrogen
URI: MIXS:0000310
"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":"name: carb_nitro_ratio\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nmultivalued: false\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe area of the ceiling space within the room
URI: MIXS:0000148
"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":"name: ceil_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nmultivalued: false\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000779
"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":"name: ceil_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nmultivalued: false\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\n\nThe type of material used to finish a ceiling
URI: MIXS:0000780
"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":"name: ceil_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nmultivalued: false\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\n\nThe construction format of the ceiling
URI: MIXS:0000782
"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":"name: ceil_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nmultivalued: false\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe feel, appearance, or consistency of a ceiling surface
URI: MIXS:0000783
"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":"name: ceil_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nmultivalued: false\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\n\nThe ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
URI: MIXS:0000143
"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":"name: ceil_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n Generally this means concrete that is exposed. A metal deck that supports a concrete\n slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nmultivalued: false\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of ceiling according to the ceiling's appearance or construction
URI: MIXS:0000784
"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":"name: ceil_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nmultivalued: false\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\n\nSigns of the presence of mold or mildew on the ceiling
URI: MIXS:0000781
"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":"name: ceil_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nmultivalued: false\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
URI: MIXS:0000751
"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":"Range: ControlledTermValue
Multivalued: True
name: chem_administration\nannotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nmultivalued: true\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nTreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens
URI: MIXS:0000555
"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: chem_mutagen\nannotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nmultivalued: true\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\n\nA measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite
URI: MIXS:0000656
"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: chem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nmultivalued: false\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)
URI: MIXS:0000457
"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":"name: chem_treat_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nmultivalued: false\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\n\nList of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included
URI: MIXS:0001012
"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":"name: chem_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the product\n and name of the supplier should be provided. The date of administration should also\n be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nmultivalued: false\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nfrom reaction participant class
URI: nmdc:chemical
"},{"location":"chemical/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionParticipant Instances of this link a reaction to a chemical entity participant no"},{"location":"chemical/#properties","title":"Properties","text":"name: chemical\ndescription: from reaction participant class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical\ndomain_of:\n- ReactionParticipant\nrange: ChemicalEntity\n\nA generic grouping for molecular formulae and empirical formulae
URI: nmdc:chemical_formula
"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":"name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\nTool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.
URI: MIXS:0000052
"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":"name: chimera_check\nannotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nmultivalued: false\nalias: chimera_check\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nConcentration of chloride in the sample
URI: MIXS:0000429
"},{"location":"chloride/#inheritance","title":"Inheritance","text":"name: chloride\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nmultivalued: false\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of chlorophyll
URI: MIXS:0000177
"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":"name: chlorophyll\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nmultivalued: false\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTreatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
URI: MIXS:0001040
"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: climate_environment\nannotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nmultivalued: true\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe Site from which a Biosample was collected
URI: nmdc:collected_from
"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collected_from/#properties","title":"Properties","text":"name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Biosample\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\nURI: nmdc:collected_into
"},{"location":"collected_into/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity yes"},{"location":"collected_into/#properties","title":"Properties","text":"name: collected_into\ntitle: collected into\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_into\ndomain_of:\n- MaterialSamplingActivity\nrange: MaterialContainer\ninlined: true\n\nURI: nmdc:collecting_biosamples_from_site_set
"},{"location":"collecting_biosamples_from_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"collecting_biosamples_from_site_set/#properties","title":"Properties","text":"Range: CollectingBiosamplesFromSite
Multivalued: True
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Database\nmultivalued: true\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\ninlined: true\ninlined_as_list: true\n\nThe time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
URI: MIXS:0000011
"},{"location":"collection_date/#inheritance","title":"Inheritance","text":"name: collection_date\nannotations:\n expected_value:\n tag: expected_value\n value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n interval. In case no exact time is available, the date/time can be right truncated\n i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nmultivalued: false\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nDate the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_date_inc
"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe time of sampling, either as an instance (single point) or interval.
URI: nmdc:collection_time
"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_time_inc
"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:community
"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":"name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:completeness
"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"completeness/#properties","title":"Properties","text":"name: completeness\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- MagBin\nrange: float\n\nURI: nmdc:completion_date
"},{"location":"completion_date/#properties","title":"Properties","text":"name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\nIf provided, specifies the compression type
URI: nmdc:compression_type
"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":"name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\nElectrical conductivity of water
URI: MIXS:0000692
"},{"location":"conduc/#inheritance","title":"Inheritance","text":"name: conduc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nmultivalued: false\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:container_size
"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialContainer no"},{"location":"container_size/#properties","title":"Properties","text":"name: container_size\ntitle: container size\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: container_size\ndomain_of:\n- MaterialContainer\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:container_type
"},{"location":"container_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialContainer no"},{"location":"container_type/#properties","title":"Properties","text":"name: container_type\ntitle: container type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: container_type\ndomain_of:\n- MaterialContainer\nrange: ContainerTypeEnum\n\nURI: nmdc:contamination
"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"contamination/#properties","title":"Properties","text":"name: contamination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- MagBin\nrange: float\n\nTotal size in bp of all contigs.
URI: nmdc:contig_bp
"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":"name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase
URI: nmdc:contigs
"},{"location":"contigs/#inheritance","title":"Inheritance","text":"name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe cooling system identifier
URI: MIXS:0000785
"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":"name: cool_syst_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nmultivalued: false\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nbasic fields
URI: nmdc:core_field
"},{"location":"core_field/#inheritance","title":"Inheritance","text":"name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:count
"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"count/#properties","title":"Properties","text":"name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\n\nthis project was made using the LinkML framework
"},{"location":"crop_rotation/","title":"Slot: crop_rotation","text":"Whether or not crop is rotated, and if yes, rotation schedule
URI: MIXS:0000318
"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":"name: crop_rotation\nannotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nmultivalued: false\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\n\nGiven a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
URI: nmdc:ctg_l50
"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":"name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
URI: nmdc:ctg_l90
"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":"name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all contigs of that length or longer contains\n at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_logsum
"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":"name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_max
"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":"name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.
URI: nmdc:ctg_n50
"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":"name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
URI: nmdc:ctg_n90
"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":"name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:ctg_powsum
"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":"name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nName or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.
URI: MIXS:0001041
"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":"name: cult_root_med\nannotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n can be the name of a commonly used medium or reference to a specific medium, e.g.\n Murashige and Skoog medium. If the medium has not been formally published, use the\n rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nmultivalued: false\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\n\nPresent state of sample site
URI: MIXS:0001080
"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":"name: cur_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nmultivalued: false\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\n\nVegetation classification from one or more standard classification systems, or agricultural crop
URI: MIXS:0000312
"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":"name: cur_vegetation\nannotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nmultivalued: false\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in vegetation classification
URI: MIXS:0000314
"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":"name: cur_vegetation_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nmultivalued: false\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of data objects within it.
URI: nmdc:data_object_set
"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":"Range: DataObject
Multivalued: True
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\ninlined: true\ninlined_as_list: true\n\nThe type of file represented by the data object.
URI: nmdc:data_object_type
"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":"name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: file type enum\n\nOne or more DOIs that links a study, or similar entity, to the generated data.
URI: nmdc:dataset_dois
"},{"location":"dataset_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: dataset_dois\ndescription: One or more DOIs that links a study, or similar entity, to the generated\n data.\nexamples:\n- value: doi:10.15485/1577267\n description: dataset_dois link to data encoded in a defined structure (as defined\n by DataCite). Should not be used to link to publications or administrative information\n like funding requests or awards.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: dataset_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nfrom database class
URI: nmdc:date_created
"},{"location":"date_created/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data yes"},{"location":"date_created/#properties","title":"Properties","text":"name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\ndomain_of:\n- Database\nrange: string\n\nThe date of the last time it rained
URI: MIXS:0000786
"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":"name: date_last_rain\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nmultivalued: false\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nDensity of the sample, which is its mass per unit volume (aka volumetric mass density)
URI: MIXS:0000435
"},{"location":"density/#inheritance","title":"Inheritance","text":"name: density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nmultivalued: false\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMain depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000992
"},{"location":"depos_env/#inheritance","title":"Inheritance","text":"name: depos_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nmultivalued: false\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\n\nThe vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
URI: MIXS:0000018
"},{"location":"depth/#inheritance","title":"Inheritance","text":"name: depth\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth can\n be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nmultivalued: false\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\na human-readable description of a thing
URI: dcterms:description
"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes NamedThing a databased entity or concept/class no ImageValue An attribute value representing an image no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CollectingBiosamplesFromSite no DataObject An object that primarily consists of symbols that represent information yes Biosample Biological source material which can be characterized by an experiment no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no MaterialEntity no ProcessedSample no AnalyticalSample no Site no PlannedProcess no OntologyClass no EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"description/#properties","title":"Properties","text":"name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- Study\n- NamedThing\n- ImageValue\nrange: string\n\nURI: nmdc:device_type
"},{"location":"device_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LabDevice no"},{"location":"device_type/#properties","title":"Properties","text":"name: device_type\ntitle: device type\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker type\nrank: 1000\nalias: device_type\ndomain_of:\n- LabDevice\nrange: DeviceTypeEnum\n\nThe temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
URI: MIXS:0000129
"},{"location":"dew_point/#inheritance","title":"Inheritance","text":"name: dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nmultivalued: false\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of diether lipids; can include multiple types of diether lipids
URI: MIXS:0000178
"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: diether_lipids\nannotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nmultivalued: true\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\n\nOne of l->r, r->l, bidirectional, neutral
URI: nmdc:direction
"},{"location":"direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"direction/#properties","title":"Properties","text":"name: direction\ndescription: One of l->r, r->l, bidirectional, neutral\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: direction\ndomain_of:\n- Reaction\nrange: string\n\nWhen rendering information, this attribute to specify the order in which the information should be rendered.
URI: nmdc:display_order
"},{"location":"display_order/#inheritance","title":"Inheritance","text":"name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: display_order\ndomain_of:\n- ImageValue\nrange: string\n\nConcentration of dissolved carbon dioxide in the sample or liquid portion of the sample
URI: MIXS:0000436
"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":"name: diss_carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nmultivalued: false\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved hydrogen
URI: MIXS:0000179
"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":"name: diss_hydrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nmultivalued: false\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
URI: MIXS:0000434
"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":"name: diss_inorg_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nmultivalued: false\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved inorganic nitrogen
URI: MIXS:0000698
"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":"name: diss_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nmultivalued: false\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved inorganic phosphorus in the sample
URI: MIXS:0000106
"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":"name: diss_inorg_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nmultivalued: false\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved iron in the sample
URI: MIXS:0000139
"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":"name: diss_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nmultivalued: false\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
URI: MIXS:0000433
"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":"name: diss_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nmultivalued: false\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
URI: MIXS:0000162
"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":"name: diss_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nmultivalued: false\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved oxygen
URI: MIXS:0000119
"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":"name: diss_oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nmultivalued: false\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
URI: MIXS:0000438
"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":"name: diss_oxygen_fluid\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nmultivalued: false\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:dissolution_aided_by
"},{"location":"dissolution_aided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_aided_by/#properties","title":"Properties","text":"name: dissolution_aided_by\ntitle: dissolution aided by\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker\nrank: 1000\nalias: dissolution_aided_by\ndomain_of:\n- DissolvingActivity\nrange: LabDevice\ninlined: true\n\nURI: nmdc:dissolution_reagent
"},{"location":"dissolution_reagent/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_reagent/#properties","title":"Properties","text":"name: dissolution_reagent\ntitle: dissolution reagent\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solvent\nrank: 1000\nalias: dissolution_reagent\ndomain_of:\n- DissolvingActivity\nrange: SolventEnum\n\nURI: nmdc:dissolution_volume
"},{"location":"dissolution_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolution_volume/#properties","title":"Properties","text":"name: dissolution_volume\ntitle: dissolution volume\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volume\nrank: 1000\nalias: dissolution_volume\ndomain_of:\n- DissolvingActivity\nrange: QuantityValue\ninlined: true\n\nURI: nmdc:dissolved_in
"},{"location":"dissolved_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity no"},{"location":"dissolved_in/#properties","title":"Properties","text":"name: dissolved_in\ntitle: dissolved in\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- container\nrank: 1000\nalias: dissolved_in\ndomain_of:\n- DissolvingActivity\nrange: MaterialContainer\ninlined: true\n\nURI: nmdc:dissolving_activity_set
"},{"location":"dissolving_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"dissolving_activity_set/#properties","title":"Properties","text":"Range: DissolvingActivity
Multivalued: True
name: dissolving_activity_set\ntitle: dissolving activity set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: dissolving_activity_set\ndomain_of:\n- Database\nrange: DissolvingActivity\ninlined: true\ninlined_as_list: true\n\n260/280 measurement of DNA sample purity
URI: nmdc:dna_absorb1
"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n260/230 measurement of DNA sample purity
URI: nmdc:dna_absorb2
"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\nProvide information on the site your DNA sample was collected from
URI: nmdc:dna_collect_site
"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_concentration
"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no ProcessedSample no"},{"location":"dna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nTube or plate (96-well)
URI: nmdc:dna_cont_type
"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:dna_cont_well
"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:dna_container_id
"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_dnase
"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:dna_isolate_meth
"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:dna_organisms
"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_project_contact
"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_samp_id
"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will be\n prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nSolution in which the DNA sample has been suspended
URI: nmdc:dna_sample_format
"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":"Range: DnaSampleFormatEnum
Recommended: True
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: dna_sample_format_enum\nrecommended: true\n\nGive the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:dna_sample_name
"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project
"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_name
"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_pi
"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_volume
"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nURI: nmdc:dnase_rna
"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\nA digital object identifier, which is intended to persistantly identify some resource on the web.
URI: nmdc:dois
"},{"location":"dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: dois\ndescription: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\ntodos:\n- the previous doi slot was an attribute, but attribute seems committed to biosamples\n- should we assert a parent term here?\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite pdf, on pp48-53 as\n of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\naliases:\n- DOIs\n- digital object identifiers\nrank: 1000\nabstract: true\nmultivalued: true\nalias: dois\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe composite type of the door
URI: MIXS:0000795
"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":"name: door_comp_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nmultivalued: false\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\n\nThe phsical condition of the door
URI: MIXS:0000788
"},{"location":"door_cond/#inheritance","title":"Inheritance","text":"name: door_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nmultivalued: false\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\n\nThe direction the door opens
URI: MIXS:0000789
"},{"location":"door_direct/#inheritance","title":"Inheritance","text":"name: door_direct\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nmultivalued: false\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\n\nThe relative location of the door in the room
URI: MIXS:0000790
"},{"location":"door_loc/#inheritance","title":"Inheritance","text":"name: door_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nmultivalued: false\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\n\nThe material the door is composed of
URI: MIXS:0000791
"},{"location":"door_mat/#inheritance","title":"Inheritance","text":"name: door_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nmultivalued: false\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\n\nThe type of movement of the door
URI: MIXS:0000792
"},{"location":"door_move/#inheritance","title":"Inheritance","text":"name: door_move\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nmultivalued: false\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\n\nThe size of the door
URI: MIXS:0000158
"},{"location":"door_size/#inheritance","title":"Inheritance","text":"name: door_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nmultivalued: false\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of door material
URI: MIXS:0000794
"},{"location":"door_type/#inheritance","title":"Inheritance","text":"name: door_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nmultivalued: false\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\n\nThe type of metal door
URI: MIXS:0000796
"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":"name: door_type_metal\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nmultivalued: false\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\n\nThe type of wood door
URI: MIXS:0000797
"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":"name: door_type_wood\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nmultivalued: false\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\n\nSigns of the presence of mold or mildew on a door
URI: MIXS:0000793
"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":"name: door_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nmultivalued: false\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nVisible waveband radiance and irradiance measurements in the water column
URI: MIXS:0000703
"},{"location":"down_par/#inheritance","title":"Inheritance","text":"name: down_par\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square centimeter\n per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nmultivalued: false\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDrainage classification from a standard system such as the USDA system
URI: MIXS:0001085
"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":"name: drainage_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nmultivalued: false\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\n\nThe buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
URI: MIXS:0000798
"},{"location":"drawings/#inheritance","title":"Inheritance","text":"name: drawings\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nmultivalued: false\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\n\nAn ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.
URI: nmdc:ecosystem
"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":"name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n and all the organisms (biotic factors) that interact with this environment. Ecosystem\n is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism or environmental\n sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n and Engineered. They represent samples collected from a natural environment or from\n another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.
URI: nmdc:ecosystem_category
"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":"name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n specific characteristics of the environment from where an organism or sample is\n isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or phyla\n and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nA unique id representing the GOLD classifiers associated with a sample.
URI: nmdc:ecosystem_path_id
"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":"name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\nEcosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.
URI: nmdc:ecosystem_subtype
"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":"name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.
URI: nmdc:ecosystem_type
"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":"name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still broad\n but specific to the characteristics of a given environment. Ecosystem type is in\n position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nPercentage of volatile solids removed from the anaerobic digestor
URI: MIXS:0000657
"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":"name: efficiency_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nmultivalued: false\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nElevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.
URI: MIXS:0000093
"},{"location":"elev/#inheritance","title":"Inheritance","text":"name: elev\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the surface,\n such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nmultivalued: false\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: QuantityValue\n\nThe number of elevators within the built structure
URI: MIXS:0000799
"},{"location":"elevator/#inheritance","title":"Inheritance","text":"name: elevator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nmultivalued: false\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\n\nAn email address for an entity such as a person. This should be the primary email address used.
URI: schema:email
"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":"name: email\ndescription: An email address for an entity such as a person. This should be the primary\n email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\nIf true, the data are embargoed and not available for public access.
URI: nmdc:embargoed
"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":"Range: Boolean
Recommended: True
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may nto be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\nA list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.
URI: nmdc:emsl_biosample_identifiers
"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nmultivalued: true\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:emsl_identifiers
"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_dois One or more DOIs that links to an EMSL Research Campaign page None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\nOne or more DOIs that links to an EMSL Research Campaign page.
URI: nmdc:emsl_project_dois
"},{"location":"emsl_project_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: emsl_project_dois\ndescription: One or more DOIs that links to an EMSL Research Campaign page.\ntitle: EMSL Project DOI\ntodos:\n- Make as a subproperty of award_dois\nexamples:\n- value: doi:10.46936/intm.proj.2021.6014\n description: emsl_project_dois link to the document outlining the EMSL specific\n award for the project. Should not be used to link to datasets or publications.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmixins:\n- emsl_identifiers\nmultivalued: true\nalias: emsl_project_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe temperature at which the sample should be stored upon delivery to EMSL
URI: nmdc:emsl_store_temp
"},{"location":"emsl_store_temp/#properties","title":"Properties","text":"Range: String
Recommended: True
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\nAmount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
URI: MIXS:0000660
"},{"location":"emulsions/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: emulsions\nannotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nmultivalued: true\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA
URI: nmdc:encodes
"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":"name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n a CDS feature or gene feature which will encode a protein. It can also be used by\n a nc transcript ot gene feature that encoded a ncRNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\nThe end of the feature in positive 1-based integer coordinates
URI: nmdc:end
"},{"location":"end/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was ended
URI: nmdc:end_date
"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PlannedProcess no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"end_date/#properties","title":"Properties","text":"name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nURI: nmdc:ended_at_time
"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"ended_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- Activity\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nReport the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
URI: MIXS:0000012
"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":"name: env_broad_scale\nannotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n or more pipes.\ndescription: 'Report the major environmental system the sample or specimen came from.\n The system(s) identified should have a coarse spatial grain, to provide the general\n environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample\n from the photic zone in middle of the Atlantic Ocean\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nmultivalued: false\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nReport the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
URI: MIXS:0000013
"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":"name: env_local_scale\nannotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at time\n of sampling.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: 'litter layer [ENVO:01000338]; Annotating a pooled sample taken from various\n vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer\n [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer\n [ENVO:01000336].'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nmultivalued: false\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nReport the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
URI: MIXS:0000014
"},{"location":"env_medium/#inheritance","title":"Inheritance","text":"name: env_medium\nannotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend subclasses\n of environmental material [ENVO:00010483].\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n or specimen at the time of sampling. We recommend using subclasses of ''environmental\n material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: 'soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the\n Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck\n on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005]'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nmultivalued: false\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nMIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
URI: nmdc:env_package
"},{"location":"env_package/#inheritance","title":"Inheritance","text":"name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the name\n of the environmental package, a selection of fields can be made from the subtables\n and can be reported\nin_subset:\n- mixs extension\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nis_a: attribute\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\nfield describing environmental aspect of a sample
URI: nmdc:environment_field
"},{"location":"environment_field/#inheritance","title":"Inheritance","text":"name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\nThe number of escalators within the built structure
URI: MIXS:0000800
"},{"location":"escalator/#inheritance","title":"Inheritance","text":"name: escalator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nmultivalued: false\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of ESS-DIVE dataset DOIs
URI: nmdc:ess_dive_datasets
"},{"location":"ess_dive_datasets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"ess_dive_datasets/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: ess_dive_datasets\ndescription: List of ESS-DIVE dataset DOIs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: ess_dive_datasets\ndomain_of:\n- Study\nrange: string\n\nConcentration of ethylbenzene in the sample
URI: MIXS:0000155
"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":"name: ethylbenzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nmultivalued: false\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nfrom database class
URI: nmdc:etl_software_version
"},{"location":"etl_software_version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data yes"},{"location":"etl_software_version/#properties","title":"Properties","text":"name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\ndomain_of:\n- Database\nrange: string\n\nURI: nmdc:execution_resource
"},{"location":"execution_resource/#inheritance","title":"Inheritance","text":"name: execution_resource\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: execution_resource\ndomain_of:\n- WorkflowExecutionActivity\nrange: string\n\nThe amount of exposed ductwork in the room
URI: MIXS:0000144
"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":"name: exp_duct\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nmultivalued: false\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of exposed pipes in the room
URI: MIXS:0000220
"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":"name: exp_pipe\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nmultivalued: false\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nExperimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
URI: MIXS:0000008
"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":"name: experimental_factor\nannotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in an\n increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nmultivalued: false\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nOther details about your sample that you feel can't be accurately represented in the available columns.
URI: nmdc:experimental_factor_other
"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":"Range: String
Recommended: True
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe number of exterior doors in the built structure
URI: MIXS:0000170
"},{"location":"ext_door/#inheritance","title":"Inheritance","text":"name: ext_door\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nmultivalued: false\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe orientation of the exterior wall
URI: MIXS:0000817
"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":"name: ext_wall_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nmultivalued: false\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\n\nThe compass direction the exterior window of the room is facing
URI: MIXS:0000818
"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":"name: ext_window_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nmultivalued: false\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\n\nLink to corresponding identifier in external database
URI: nmdc:external_database_identifiers
"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nmultivalued: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:extraction_method
"},{"location":"extraction_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_method/#properties","title":"Properties","text":"name: extraction_method\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: extraction_method\ndomain_of:\n- Extraction\nrange: string\n\nThis property links a database object to the set of extractions within it.
URI: nmdc:extraction_set
"},{"location":"extraction_set/#inheritance","title":"Inheritance","text":"Range: Extraction
Multivalued: True
name: extraction_set\ndescription: This property links a database object to the set of extractions within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: extraction_set\ndomain_of:\n- Database\nrange: Extraction\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:extraction_target
"},{"location":"extraction_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_target/#properties","title":"Properties","text":"name: extraction_target\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: extraction_target\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\n\nUnusual physical events that may have affected microbial populations
URI: MIXS:0000320
"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":"name: extreme_event\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nmultivalued: false\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nSoil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
URI: MIXS:0001083
"},{"location":"fao_class/#inheritance","title":"Inheritance","text":"name: fao_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nmultivalued: false\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\n\nTODO: Yuri to write
URI: nmdc:feature_type
"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":"name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\nInformation about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens
URI: MIXS:0000556
"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fertilizer_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nmultivalued: true\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nName of the hydrocarbon field (e.g. Albacora)
URI: MIXS:0000291
"},{"location":"field/#inheritance","title":"Inheritance","text":"name: field\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nmultivalued: false\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:field_research_site_set
"},{"location":"field_research_site_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"field_research_site_set/#properties","title":"Properties","text":"Range: FieldResearchSite
Multivalued: True
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Database\nmultivalued: true\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\ninlined: true\ninlined_as_list: true\n\nSize of the file in bytes
URI: nmdc:file_size_bytes
"},{"location":"file_size_bytes/#inheritance","title":"Inheritance","text":"name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\nType of filter used or how the sample was filtered
URI: nmdc:filter_method
"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":"Range: String
Recommended: True
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nA device which removes solid particulates or airborne molecular contaminants
URI: MIXS:0000765
"},{"location":"filter_type/#inheritance","title":"Inheritance","text":"Range: FilterTypeEnum
Multivalued: True
name: filter_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nmultivalued: true\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\n\nHistorical and/or physical evidence of fire
URI: MIXS:0001086
"},{"location":"fire/#inheritance","title":"Inheritance","text":"name: fire\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nmultivalued: false\nalias: fire\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nA firebox with chimney
URI: MIXS:0000802
"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":"name: fireplace_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nmultivalued: false\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nHistorical and/or physical evidence of flooding
URI: MIXS:0000319
"},{"location":"flooding/#inheritance","title":"Inheritance","text":"name: flooding\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nmultivalued: false\nalias: flooding\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nThe time period since installment of the carpet or flooring
URI: MIXS:0000164
"},{"location":"floor_age/#inheritance","title":"Inheritance","text":"name: floor_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nmultivalued: false\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe area of the floor space within the room
URI: MIXS:0000165
"},{"location":"floor_area/#inheritance","title":"Inheritance","text":"name: floor_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nmultivalued: false\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000803
"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":"name: floor_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nmultivalued: false\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\n\nThe number of floors in the building, including basements and mechanical penthouse
URI: MIXS:0000225
"},{"location":"floor_count/#inheritance","title":"Inheritance","text":"name: floor_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nmultivalued: false\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe floor covering type; the finished surface that is walked on
URI: MIXS:0000804
"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":"name: floor_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nmultivalued: false\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\n\nRefers to the structural elements and subfloor upon which the finish flooring is installed
URI: MIXS:0000806
"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":"name: floor_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nmultivalued: false\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\n\nThe ability of the floor to provide inertia against temperature fluctuations
URI: MIXS:0000166
"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":"name: floor_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nmultivalued: false\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSigns of the presence of mold or mildew in a room
URI: MIXS:0000805
"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":"name: floor_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nmultivalued: false\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\n\nRaw or converted fluorescence of water
URI: MIXS:0000704
"},{"location":"fluor/#inheritance","title":"Inheritance","text":"name: fluor\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nmultivalued: false\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
URI: MIXS:0000226
"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":"name: freq_clean\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nmultivalued: false\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of times a meal is cooked per week
URI: MIXS:0000227
"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":"name: freq_cook\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nmultivalued: false\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:functional_annotation_agg
"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":"Range: FunctionalAnnotationAggMember
Multivalued: True
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of all functional annotations
URI: nmdc:functional_annotation_set
"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":"Range: FunctionalAnnotation
Multivalued: True
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\ninlined: true\ninlined_as_list: true\n\nA list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.
URI: nmdc:funding_sources
"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process applications\n and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nmultivalued: true\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\n\nInformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens
URI: MIXS:0000557
"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fungicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nmultivalued: true\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe types of furniture present in the sampled room
URI: MIXS:0000807
"},{"location":"furniture/#inheritance","title":"Inheritance","text":"name: furniture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nmultivalued: false\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\n\nThe gap size percentage of all scaffolds.
URI: nmdc:gap_pct
"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":"name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nUse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
URI: MIXS:0000558
"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_environment\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nmultivalued: true\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nAmount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
URI: MIXS:0000661
"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_substances\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nmultivalued: true\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\n\nAverage of GC content of all contigs.
URI: nmdc:gc_avg
"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":"name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nStandard deviation of GC content of all contigs.
URI: nmdc:gc_std
"},{"location":"gc_std/#inheritance","title":"Inheritance","text":"name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe gender type of the restroom
URI: MIXS:0000808
"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":"name: gender_restroom\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nmultivalued: false\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\n\nURI: nmdc:gene_count
"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":"name: gene_count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:gene_function_id
"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":"name: gene_function_id\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\n\nGenetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection
URI: MIXS:0000859
"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":"name: genetic_mod\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nmultivalued: false\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of all features
URI: nmdc:genome_feature_set
"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":"Range: GenomeFeature
Multivalued: True
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\ninlined: true\ninlined_as_list: true\n\nThe geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)
URI: MIXS:0000010
"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":"name: geo_loc_name\nannotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n name followed by specific region name. Country or sea names should be chosen from\n the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nmultivalued: false\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nA positive 1-based integer coordinate indicating start or end
URI: nmdc:gff_coordinate
"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n plasmids, and some viral genomes), the requirement for start to be less than or\n equal to end is satisfied by making end = the position of the end + the length of\n the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\nURI: nmdc:git_url
"},{"location":"git_url/#inheritance","title":"Inheritance","text":"name: git_url\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: git_url\ndomain_of:\n- WorkflowExecutionActivity\nrange: string\n\nMeasurement of glucosidase activity
URI: MIXS:0000137
"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":"name: glucosidase_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nmultivalued: false\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:gnps_identifiers
"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\nidentifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results
URI: nmdc:gnps_task_identifiers
"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gnps\\.task:[a-f0-9]+$
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysisActivity/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nmultivalued: true\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^gnps\\.task:[a-f0-9]+$\n\nidentifiers for corresponding analysis project in GOLD
URI: nmdc:gold_analysis_project_identifiers
"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Ga[0-9]+$
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotationActivity\n- MetatranscriptomeAnnotationActivity\nrange: external_identifier\npattern: ^gold:Ga[0-9]+$\n\nidentifiers for corresponding sample in GOLD
URI: nmdc:gold_biosample_identifiers
"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gb[0-9]+$
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^gold:Gb[0-9]+$\n\nURI: nmdc:gold_identifiers
"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD None Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None OmicsProcessing gold_analysis_project_identifiers identifiers for corresponding analysis project in GOLD None MetagenomeAnnotationActivity, MetatranscriptomeAnnotationActivity"},{"location":"gold_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\nThis is a grouping for any of the gold path fields
URI: nmdc:gold_path_field
"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":"name: gold_path_field\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nabstract: true\nalias: gold_path_field\nrange: string\n\nidentifiers for corresponding sequencing project in GOLD
URI: nmdc:gold_sequencing_project_identifiers
"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gp[0-9]+$
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- OmicsProcessing\nrange: external_identifier\npattern: ^gold:Gp[0-9]+$\n\nidentifiers for corresponding project(s) in GOLD
URI: nmdc:gold_study_identifiers
"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gs[0-9]+$
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nmultivalued: true\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^gold:Gs[0-9]+$\n\nWhether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
URI: MIXS:0000875
"},{"location":"gravidity/#inheritance","title":"Inheritance","text":"name: gravidity\nannotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nmultivalued: false\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments
URI: MIXS:0000559
"},{"location":"gravity/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gravity\nannotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nmultivalued: true\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research
URI: MIXS:0001043
"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":"name: growth_facil\nannotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nmultivalued: false\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nCharacteristic shape, appearance or growth form of a plant species
URI: MIXS:0001044
"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":"name: growth_habit\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nmultivalued: false\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\n\nInformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens
URI: MIXS:0000560
"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: growth_hormone_regm\nannotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple growth hormone\n regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nmultivalued: true\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:gtdbtk_class
"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":"name: gtdbtk_class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_domain
"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":"name: gtdbtk_domain\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_family
"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":"name: gtdbtk_family\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_genus
"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":"name: gtdbtk_genus\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_order
"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":"name: gtdbtk_order\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_phylum
"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":"name: gtdbtk_phylum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:gtdbtk_species
"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":"name: gtdbtk_species\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:habitat
"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"habitat/#properties","title":"Properties","text":"name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\nThe total count of hallways and cooridors in the built structure
URI: MIXS:0000228
"},{"location":"hall_count/#inheritance","title":"Inheritance","text":"name: hall_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nmultivalued: false\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe handidness of the individual sampled
URI: MIXS:0000809
"},{"location":"handidness/#inheritance","title":"Inheritance","text":"name: handidness\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nmultivalued: false\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\n\nLinks a quantity value to a boolean
URI: nmdc:has_boolean_value
"},{"location":"has_boolean_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BooleanValue A value that is a boolean no"},{"location":"has_boolean_value/#properties","title":"Properties","text":"name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: false\nalias: has_boolean_value\ndomain_of:\n- BooleanValue\nrange: boolean\n\nA reference to a file that holds calibration information.
URI: nmdc:has_calibration
"},{"location":"has_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_calibration/#properties","title":"Properties","text":"name: has_calibration\ndescription: A reference to a file that holds calibration information.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_calibration\ndomain_of:\n- MetabolomicsAnalysisActivity\n- NomAnalysisActivity\nrange: string\n\nThis slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study
URI: prov:qualifiedAssociation
"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":"Range: CreditAssociation
Multivalued: True
name: has_credit_associations\nannotations:\n display_hint:\n tag: display_hint\n value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\nnotes:\n- 'had just been \"inlined: true\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Study\nslot_uri: prov:qualifiedAssociation\nmultivalued: true\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_function
"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":"Range: String
Regex pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\nAn input to a process.
URI: nmdc:has_input
"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes PlannedProcess no Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes CollectingBiosamplesFromSite yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_input/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\ndomain: NamedThing\nmultivalued: true\nalias: has_input\ndomain_of:\n- BiosampleProcessing\n- OmicsProcessing\n- WorkflowExecutionActivity\n- PlannedProcess\nrange: NamedThing\n\nThe maximum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_maximum_numeric_value
"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: float\n\nURI: nmdc:has_metabolite_quantifications
"},{"location":"has_metabolite_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysisActivity no"},{"location":"has_metabolite_quantifications/#properties","title":"Properties","text":"Range: MetaboliteQuantification
Multivalued: True
name: has_metabolite_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_metabolite_quantifications\ndomain_of:\n- MetabolomicsAnalysisActivity\nrange: MetaboliteQuantification\n\nThe minimum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_minimum_numeric_value
"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: float\n\nURI: nmdc:has_numeric_value
"},{"location":"has_numeric_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_numeric_value/#properties","title":"Properties","text":"name: has numeric value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_numeric_value\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: double\n\nAn output biosample to a processing step
URI: nmdc:has_output
"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes PlannedProcess no Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes CollectingBiosamplesFromSite yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"has_output/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_output\ndescription: An output biosample to a processing step\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\ndomain: NamedThing\nmultivalued: true\nalias: has_output\ndomain_of:\n- OmicsProcessing\n- WorkflowExecutionActivity\n- PlannedProcess\nrange: NamedThing\n\nA pathway can be broken down to a series of reaction step
URI: nmdc:has_part
"},{"location":"has_part/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no"},{"location":"has_part/#properties","title":"Properties","text":"Range: Reaction
Multivalued: True
name: has_part\ndescription: A pathway can be broken down to a series of reaction step\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_part\ndomain_of:\n- Pathway\nrange: Reaction\n\nURI: nmdc:has_participants
"},{"location":"has_participants/#inheritance","title":"Inheritance","text":"name: has_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- RO:0000057\nrank: 1000\nabstract: true\nalias: has_participants\nrange: string\n\nURI: nmdc:has_peptide_quantifications
"},{"location":"has_peptide_quantifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysisActivity no"},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":"Range: PeptideQuantification
Multivalued: True
name: has_peptide_quantifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: has_peptide_quantifications\ndomain_of:\n- MetaproteomicsAnalysisActivity\nrange: PeptideQuantification\n\nURI: nmdc:has_raw_value
"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_raw_value/#properties","title":"Properties","text":"name: has raw value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nstring_serialization: '{has numeric value} {has unit}'\nalias: has_raw_value\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: string\n\nExample \"m\"
URI: nmdc:has_unit
"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"has_unit/#properties","title":"Properties","text":"name: has unit\ndescription: Example \"m\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_unit\nowner: QuantityValue\ndomain_of:\n- Biosample\nrange: string\n\nMain hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000989
"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":"name: hc_produced\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nmultivalued: false\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\n\nMain Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000988
"},{"location":"hcr/#inheritance","title":"Inheritance","text":"name: hcr\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n as a natural environmental feature containing large amounts of hydrocarbons at high\n concentrations potentially suitable for commercial exploitation. This term should\n not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n environments with currently limited commercial interest such as seeps, outcrops,\n gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nmultivalued: false\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\n\nOriginal formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS
URI: MIXS:0000406
"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":"name: hcr_fw_salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nmultivalued: false\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nGeological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period(geology)). If \"other\" is specified, please propose entry in \"additional info\" field_
URI: MIXS:0000993
"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":"name: hcr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nmultivalued: false\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\n\nOriginal pressure of the hydrocarbon resource
URI: MIXS:0000395
"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":"name: hcr_pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nmultivalued: false\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\n\nOriginal temperature of the hydrocarbon resource
URI: MIXS:0000393
"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":"name: hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nmultivalued: false\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\n\nMethods of conditioning or heating a room or building
URI: MIXS:0000766
"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":"Range: HeatCoolTypeEnum
Multivalued: True
name: heat_cool_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nmultivalued: true\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\n\nThe location of heat delivery within the room
URI: MIXS:0000810
"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":"name: heat_deliv_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nmultivalued: false\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\n\nThe method by which the heat is delivered through the system
URI: MIXS:0000812
"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":"name: heat_sys_deliv_meth\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nmultivalued: false\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\n\nThe heating system identifier
URI: MIXS:0000833
"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":"name: heat_system_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nmultivalued: false\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nHeavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.
URI: MIXS:0000652
"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: heavy_metals\nannotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nmultivalued: true\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\n\nReference or method used in determining heavy metals
URI: MIXS:0000343
"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":"name: heavy_metals_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nmultivalued: false\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average carpet fiber height in the indoor environment
URI: MIXS:0000167
"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":"name: height_carper_fiber\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nmultivalued: false\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000561
"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: herbicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of herbicide,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nmultivalued: true\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:highest_similarity_score
"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":"name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteQuantification\nrange: float\n\nThe purpose of the NMDC Schema is to define metadata for the National Microbiome Data Collaborative (NMDC). The NMDC is a multi-organizational effort to enable integrated microbiome data across diverse areas in medicine, agriculture, bioenergy, and the environment. This integrated platform facilitates comprehensive discovery of and access to multidisciplinary microbiome data in order to unlock new possibilities with microbiome data science.
The NMDC schema is used during the translation process to specify how metadata elements are related.
"},{"location":"horizon_meth/","title":"Slot: horizon_meth","text":"Reference or method used in determining the horizon
URI: MIXS:0000321
"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":"name: horizon_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nmultivalued: false\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nAge of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees
URI: MIXS:0000255
"},{"location":"host_age/#inheritance","title":"Inheritance","text":"name: host_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nmultivalued: false\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal body habitat where the sample was obtained from
URI: MIXS:0000866
"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":"name: host_body_habitat\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nmultivalued: false\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\n\nSubstance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon
URI: MIXS:0000888
"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":"name: host_body_product\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: Portion of mucus [fma66938]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nmultivalued: false\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nName of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
URI: MIXS:0000867
"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":"name: host_body_site\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nmultivalued: false\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nCore body temperature of the host when sample was collected
URI: MIXS:0000274
"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":"name: host_body_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nmultivalued: false\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe color of host
URI: MIXS:0000260
"},{"location":"host_color/#inheritance","title":"Inheritance","text":"name: host_color\nannotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nmultivalued: false\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\n\nCommon name of the host.
URI: MIXS:0000248
"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":"name: host_common_name\nannotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nmultivalued: false\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
URI: MIXS:0000869
"},{"location":"host_diet/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_diet\nannotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nmultivalued: true\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of dry mass
URI: MIXS:0000257
"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":"name: host_dry_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nmultivalued: false\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nFamilial relationships to other hosts in the same study; can include multiple relationships
URI: MIXS:0000872
"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_family_relation\nannotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\ndescription: Familial relationships to other hosts in the same study; can include\n multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nmultivalued: true\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\n\nObserved genotype
URI: MIXS:0000365
"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":"name: host_genotype\nannotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nmultivalued: false\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\n\nLiterature reference giving growth conditions of the host
URI: MIXS:0000871
"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":"name: host_growth_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nmultivalued: false\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe height of subject
URI: MIXS:0000264
"},{"location":"host_height/#inheritance","title":"Inheritance","text":"name: host_height\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nmultivalued: false\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nContent of last meal and time since feeding; can include multiple values
URI: MIXS:0000870
"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_last_meal\nannotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nmultivalued: true\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe length of subject
URI: MIXS:0000256
"},{"location":"host_length/#inheritance","title":"Inheritance","text":"name: host_length\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nmultivalued: false\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDescription of life stage of host
URI: MIXS:0000251
"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":"name: host_life_stage\nannotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nmultivalued: false\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:host_name
"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":"name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\nPhenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
URI: MIXS:0000874
"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":"name: host_phenotype\nannotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nmultivalued: false\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nGender or physical sex of the host.
URI: MIXS:0000811
"},{"location":"host_sex/#inheritance","title":"Inheritance","text":"name: host_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nmultivalued: false\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\n\nMorphological shape of host
URI: MIXS:0000261
"},{"location":"host_shape/#inheritance","title":"Inheritance","text":"name: host_shape\nannotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nmultivalued: false\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\n\nA unique identifier by which each subject can be referred to, de-identified.
URI: MIXS:0000861
"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":"name: host_subject_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nmultivalued: false\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.
URI: MIXS:0001318
"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_subspecf_genlin\nannotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nmultivalued: true\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\n\nThe growth substrate of the host.
URI: MIXS:0000252
"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":"name: host_substrate\nannotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nmultivalued: false\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
URI: MIXS:0001298
"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_symbiont\nannotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nmultivalued: true\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\n\nNCBI taxon id of the host, e.g. 9606
URI: MIXS:0000250
"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":"name: host_taxid\nannotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nmultivalued: false\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nTotal mass of the host at collection, the unit depends on host
URI: MIXS:0000263
"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":"name: host_tot_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nmultivalued: false\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of wet mass
URI: MIXS:0000567
"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":"name: host_wet_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nmultivalued: false\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nAmount of water vapour in the air, at the time of sampling
URI: MIXS:0000100
"},{"location":"humidity/#inheritance","title":"Inheritance","text":"name: humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nmultivalued: false\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000568
"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: humidity_regm\nannotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying degree of\n humidity; information about treatment involving use of growth hormones; should include\n amount of humidity administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end time\n of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nmultivalued: true\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nA unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
URI: nmdc:id
"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes Study A study summarizes the overall goal of a research initiative and outlines the... yes NamedThing a databased entity or concept/class no Activity a provence-generating activity yes Pooling physical combination of several instances of like material yes Extraction A material separation in which a desired component of an input material is se... yes LibraryPreparation yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes CollectingBiosamplesFromSite yes DataObject An object that primarily consists of symbols that represent information yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetatranscriptomeAssembly yes MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeAnnotationActivity yes MetatranscriptomeActivity A metatranscriptome activity that e yes MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... yes MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis yes ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... yes ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... yes MetabolomicsAnalysisActivity yes MetaproteomicsAnalysisActivity yes NomAnalysisActivity yes MaterialEntity no ProcessedSample yes AnalyticalSample yes Site yes PlannedProcess no OntologyClass yes EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample yes FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Biosample\n- Study\n- NamedThing\n- Activity\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nIdentifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects referenced
Examples of entities that require identifiers:
Identifiers should be:
See McMurry et al, PMID:28662064 for more desiderata.
"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"Following McMurry et al we adopt the use of prefixed identifiers
The syntax is:
Prefix:LocalId\nExamples:
These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these
All prefixes should be registered with a standard identifier prefix system. These include:
Registry entry: https://registry.identifiers.org/registry/biosample
Example ID/CURIE: BIOSAMPLE:SAMEA2397676
Resolving via identifiers.org: https://identifiers.org/BIOSAMPLE:SAMEA2397676
Resolving via nt2.net: http://n2t.net/BIOSAMPLE:SAMEA2397676
"},{"location":"identifiers/#gold-identifiers","title":"GOLD identifiers","text":"https://registry.identifiers.org/registry/gold
Example ID: GOLD:Gp0119849
Resolving via identifiers.org: https://identifiers.org/GOLD:Gp0119849
"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on http://obofoundry.org
For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007
KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.
The NMDC schema is annotated with the set of IDs that are allowed to act as primary keys for instances of each class.
For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY
The underlying yaml looks like this:
orthology group:\n is_a: functional annotation term\n description: >-\n A set of genes or gene products in which all members are orthologous\n id_prefixes:\n - KEGG.ORTHOLOGY ## KO number\n - EGGNOG\n - PFAM\n - TIGRFAM\n - SUPFAM\n - PANTHER.FAMILY\n exact_mappings:\n - biolink:GeneFamily\nThe full URLs for each is in the jsonld context file
"},{"location":"identifiers/#ids-minted-for-use-within-nmdc","title":"IDs minted for use within NMDC","text":"The NMDC schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification, which is discussed below.
NMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids, but it will require an update before it generates ids following the pattern specified below.
The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC schema and metadata team.
No matter where they are minted, all NMDC id values must match this abstract pattern:
nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\nThe abstract pattern has six parts, delimited by hyphens (unless otherwise specified):
nmdc: All NMDC identifiers will begin with this static prefix.
<typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.
<shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].
<blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.
<.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.
<_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.
The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.
^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\nWe try to reuse IDs as far as possible. For example, for any sample already in GOLD, we use the GOLD sample identifier, e.g. GOLD:Gb.....
"},{"location":"identifiers/#ids-generated-during-workflows","title":"IDs generated during workflows","text":"This section is in progress. See https://github.com/microbiomedata/nmdc-metadata/issues/195
All instances of OmicsProcessing have IDs. The policy for ID depends on the provider.
Currently metagenomics omics objects look like this:
id: \"gold:Gp0108335\"\n name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n has_input:\n - \"gold:Gb0108335\"\n part_of:\n - \"gold:Gs0112340\"\n has_output:\n - \"jgi:551a20d30d878525404e90d5\"\n omics_type: Metagenome\n type: \"nmdc:OmicsProcessing\"\n add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n processing_institution: \"Joint Genome Institute\"\n principal_investigator_name: \"Virginia Rich\"\nnote that we use re-using the GOLD ID rather than minting a new one
the linked data object uses a jgi prefix and an md5 hash
id: \"jgi:551a20d30d878525404e90d5\"\n name: \"8871.1.114459.GCCAAT.fastq.gz\"\n description: \"Raw sequencer read data\"\n file_size_bytes: 17586370657\n type: \"nmdc:DataObject\"\nnote that currently jgi is not registered and thus the ID is not resolvable
Currently metaproteomics omics objects look like this:
id: \"emsl:404590\"\n name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n part_of:\n - \"gold:Gs0110132\"\n has_output:\n - \"emsl:output_404590\"\n omics_type: Proteomics\n type: \"nmdc:OmicsProcessing\"\n instrument_name: \"VOrbiETD03\"\n processing_institution: \"Environmental Molecular Sciences Lab\"\nthis is suboptimal; emsl is not yet registered, and it's not clear that the integer is unique within emsl, let alone the nmdc subset
the output data objects are formed from these:
id: \"emsl:output_404590\"\n name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n file_size_bytes: 503296678\n type: \"nmdc:DataObject\"\nthe data objects use hashes (md5) prefixed with nmdc:
name: \"404590_resultant.tsv\"\n description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n file_size_bytes: 10948480\n type: \"nmdc:DataObject\"\n id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\nnote nmdc is not yet registered
Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.
The main entity we care about in these is the [gene product] https://microbiomedata.github.io/nmdc-metadata/docs/GeneProduct) ID (usually a protein), this is what functional annotation hangs off.
This is typically a protein encoded by a CDS, e.g.
Ga0185794_41 GeneMark.hmm-2 v1.05 CDS 48 1037 56.13 + 0 ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\nCurrently we are prefixing the ID field in GFF with nmdc, e.g. nmdc:Ga0185794_41_48_1037 as the protein ID
When converting col9 we ensure that each ID is correctly prefixed. So for example, we use KEGG.OTHOLOGY:K12960 not KO:K12960 as the former is the official prefix according to KEGG and identifiers.org
We will also later need a policy for IDs for the sequences in col1 (ie genome or transcript), please return later for more details...
"},{"location":"identifiers/#mixs-term-identifiers","title":"MIxS term identifiers","text":"We are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level.
Please check this section later
For now we place these in the nmdc namespaces, e.g
nmdc:alt
Please check this section later
"},{"location":"identifiers/#identifiers-and-semantic-web-uris","title":"Identifiers and semantic web URIs","text":"We produce a JSON-LD context with the schema:
When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs
"},{"location":"igsn_biosample_identifiers/","title":"Slot: igsn_biosample_identifiers","text":"A list of identifiers for the biosample from the IGSN database.
URI: nmdc:igsn_biosample_identifiers
"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nmultivalued: true\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:igsn_identifiers
"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\nA list of identifiers that relate the biosample to records in the IMG database.
URI: nmdc:img_identifiers
"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmultivalued: true\nalias: img_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\nURI: nmdc:inchi
"},{"location":"inchi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi/#properties","title":"Properties","text":"name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\ndomain_of:\n- ChemicalEntity\nrange: string\n\nURI: nmdc:inchi_key
"},{"location":"inchi_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"inchi_key/#properties","title":"Properties","text":"name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\ndomain_of:\n- ChemicalEntity\nrange: string\n\nA distinguishable space within a structure, the purpose for which discrete areas of a building is used
URI: MIXS:0000763
"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":"name: indoor_space\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nmultivalued: false\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\n\nType of indoor surface
URI: MIXS:0000764
"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":"name: indoor_surf\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nmultivalued: false\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\n\nPercentage of industrial effluents received by wastewater treatment plant
URI: MIXS:0000662
"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":"name: indust_eff_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nmultivalued: false\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
URI: MIXS:0000664
"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: inorg_particles\nannotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nmultivalued: true\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe nucleotide base count number of input reads for QC analysis.
URI: nmdc:input_base_count
"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":"name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nURI: nmdc:input_contig_num
"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":"name: input_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nTotal mass of sample used in activity.
URI: nmdc:input_mass
"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":"name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n_TODO _
URI: nmdc:input_read_bases
"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":"name: input_read_bases\ndescription: 'TODO '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nThe sequence count number of input reads for QC analysis.
URI: nmdc:input_read_count
"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":"name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nURI: nmdc:insdc_analysis_identifiers
"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_analysis_identifiers\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\nURI: nmdc:insdc_assembly_identifiers
"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\nidentifiers for corresponding project in INSDC Bioproject
URI: nmdc:insdc_bioproject_identifiers
"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_bioproject_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\nidentifiers for corresponding sample in INSDC
URI: nmdc:insdc_biosample_identifiers
"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\nURI: nmdc:insdc_experiment_identifiers
"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_experiment_identifiers\ndomain_of:\n- OmicsProcessing\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\nAny identifier covered by the International Nucleotide Sequence Database Collaboration
URI: nmdc:insdc_identifiers
"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None OmicsProcessing insdc_analysis_identifiers None insdc_assembly_identifiers None MetagenomeAssembly, MetatranscriptomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\nsecondary identifiers for corresponding sample in INSDC
URI: nmdc:insdc_secondary_sample_identifiers
"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:(E|D|S)RS[0-9]{6,}$
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\nidentifiers for corresponding project in INSDC SRA / ENA
URI: nmdc:insdc_sra_ena_study_identifiers
"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nmultivalued: true\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\nThe recorded value at sampling time (power density)
URI: MIXS:0000168
"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":"name: inside_lux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nmultivalued: false\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe name of the instrument that was used for processing the sample.
URI: nmdc:instrument_name
"},{"location":"instrument_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no InstrumentValue no"},{"location":"instrument_name/#properties","title":"Properties","text":"name: instrument_name\ndescription: The name of the instrument that was used for processing the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_name\ndomain_of:\n- OmicsProcessing\n- InstrumentValue\nrange: string\n\nThe physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000813
"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":"name: int_wall_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nmultivalued: false\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\n\nfield describing aspect of the investigation/study to which the sample belongs
URI: nmdc:investigation_field
"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":"name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:is_balanced
"},{"location":"is_balanced/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_balanced/#properties","title":"Properties","text":"name: is_balanced\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_balanced\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_diastereoselective
"},{"location":"is_diastereoselective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_diastereoselective/#properties","title":"Properties","text":"name: is_diastereoselective\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_diastereoselective\ndomain_of:\n- Reaction\nrange: boolean\n\nFalse if includes R-groups
URI: nmdc:is_fully_characterized
"},{"location":"is_fully_characterized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_fully_characterized/#properties","title":"Properties","text":"name: is_fully_characterized\ndescription: False if includes R-groups\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_fully_characterized\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_stereo
"},{"location":"is_stereo/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_stereo/#properties","title":"Properties","text":"name: is_stereo\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stereo\ndomain_of:\n- Reaction\nrange: boolean\n\nURI: nmdc:is_transport
"},{"location":"is_transport/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"is_transport/#properties","title":"Properties","text":"name: is_transport\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_transport\ndomain_of:\n- Reaction\nrange: boolean\n\nList isotope exposure or addition applied to your sample.
URI: nmdc:isotope_exposure
"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":"Range: String
Recommended: True
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n labeled compounds\nexamples:\n- value: 13C glucose\n- value: H218O\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{termLabel} {[termID]}; {timestamp}'\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nInjection water breakthrough date per well following a secondary and/or tertiary recovery
URI: MIXS:0001010
"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":"name: iw_bt_date_well\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nmultivalued: false\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nProportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)
URI: MIXS:0000455
"},{"location":"iwf/#inheritance","title":"Inheritance","text":"name: iwf\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nmultivalued: false\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nidentifiers for entities according to JGI Portal
URI: nmdc:jgi_portal_identifiers
"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.
URI: nmdc:jgi_portal_study_identifiers
"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.proposal:\\d+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD API\n and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nmultivalued: true\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^jgi.proposal:\\d+$\n\nA list of keywords that used to associate the entity. Keywords SHOULD come from controlled vocabularies, including MESH, ENVO.
URI: nmdc:keywords
"},{"location":"keywords/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: keywords\ndescription: A list of keywords that used to associate the entity. Keywords SHOULD\n come from controlled vocabularies, including MESH, ENVO.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- dcterms:subject\nrank: 1000\nmultivalued: true\nalias: keywords\nrange: string\n\nShould use ISO 639-1 code e.g. \"en\", \"fr\"
URI: nmdc:language
"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":"name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language code\n\nThe last time the floor was cleaned (swept, mopped, vacuumed)
URI: MIXS:0000814
"},{"location":"last_clean/#inheritance","title":"Inheritance","text":"name: last_clean\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nmultivalued: false\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
URI: MIXS:0000009
"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":"name: lat_lon\nannotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nmultivalued: false\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\n\nlatitude
URI: wgs84:lat
"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":"name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\ndomain: GeolocationValue\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\nlime buffer capacity, determined after 30 minute incubation
URI: nmdc:lbc_thirty
"},{"location":"lbc_thirty/#inheritance","title":"Inheritance","text":"name: lbc_thirty\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nis_a: attribute\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nlime buffer capacity, determined at equilibrium after 5 day incubation
URI: nmdc:lbceq
"},{"location":"lbceq/#inheritance","title":"Inheritance","text":"name: lbceq\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nis_a: attribute\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:left_participants
"},{"location":"left_participants/#inheritance","title":"Inheritance","text":"Range: ReactionParticipant
Multivalued: True
name: left_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_participants\nmultivalued: true\nalias: left_participants\ndomain_of:\n- Reaction\nrange: ReactionParticipant\n\nURI: nmdc:library_preparation_kit
"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":"name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\nThis property links a database object to the set of DNA extractions within it.
URI: nmdc:library_preparation_set
"},{"location":"library_preparation_set/#inheritance","title":"Inheritance","text":"Range: LibraryPreparation
Multivalued: True
name: library_preparation_set\ndescription: This property links a database object to the set of DNA extractions within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- library_construction_set\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: library_preparation_set\ndomain_of:\n- Database\nrange: LibraryPreparation\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:library_type
"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":"name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\nMeasurement of light intensity
URI: MIXS:0000706
"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":"name: light_intensity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nmultivalued: false\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment(s) involving exposure to light, including both light intensity and quality.
URI: MIXS:0000569
"},{"location":"light_regm/#inheritance","title":"Inheritance","text":"name: light_regm\nannotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nmultivalued: false\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nApplication of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
URI: MIXS:0000769
"},{"location":"light_type/#inheritance","title":"Inheritance","text":"Range: LightTypeEnum
Multivalued: True
name: light_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n includes the use of both artificial light sources such as lamps and light fixtures,\n as well as natural illumination by capturing daylight. Can also include absence\n of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nmultivalued: true\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\n\nLink to additional analysis results performed on the sample
URI: MIXS:0000340
"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":"name: link_addit_analys\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nmultivalued: false\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\n\nLink to digitized soil maps or other soil classification information
URI: MIXS:0000329
"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":"name: link_class_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nmultivalued: false\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nLink to climate resource
URI: MIXS:0000328
"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":"name: link_climate_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nmultivalued: false\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\n\nHydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000990
"},{"location":"lithology/#inheritance","title":"Inheritance","text":"name: lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nmultivalued: false\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\n\nSoil classification based on local soil classification system
URI: MIXS:0000330
"},{"location":"local_class/#inheritance","title":"Inheritance","text":"name: local_class\nannotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nmultivalued: false\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in determining the local soil classification
URI: MIXS:0000331
"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":"name: local_class_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nmultivalued: false\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:location
"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":"name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\nlongitude
URI: wgs84:long
"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":"name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\ndomain: GeolocationValue\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal degree\n\nURI: nmdc:low_depth_contig_num
"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":"name: low_depth_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nConcentration of magnesium in the sample
URI: MIXS:0000431
"},{"location":"magnesium/#inheritance","title":"Inheritance","text":"name: magnesium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nmultivalued: false\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of MAGs analysis activities.
URI: nmdc:mags_activity_set
"},{"location":"mags_activity_set/#inheritance","title":"Inheritance","text":"Range: MagsAnalysisActivity
Multivalued: True
name: mags_activity_set\ndescription: This property links a database object to the set of MAGs analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: mags_activity_set\ndomain_of:\n- Database\nrange: MagsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:mags_list
"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":"Range: MagBin
Multivalued: True
name: mags_list\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: mags_list\ndomain_of:\n- MagsAnalysisActivity\nrange: MagBin\n\nConcentration of manganese in the sample
URI: nmdc:manganese
"},{"location":"manganese/#inheritance","title":"Inheritance","text":"name: manganese\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nis_a: attribute\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nidentifiers for entities according to MASSIVE
URI: nmdc:massive_identifiers
"},{"location":"massive_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain massive_study_identifiers identifiers for corresponding study in MASSIVE None Study"},{"location":"massive_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: massive_identifiers\ndescription: identifiers for entities according to MASSIVE\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: massive_identifiers\nrange: string\n\nidentifiers for corresponding study in MASSIVE
URI: nmdc:massive_study_identifiers
"},{"location":"massive_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^MASSIVE:
name: massive_study_identifiers\ndescription: identifiers for corresponding study in MASSIVE\ntodos:\n- prefix not defined yet\nexamples:\n- value: MASSIVE:MSV000090886\n description: MASSIVE id for MASSIVE's metabolomics analysis of Gb0305843, resolvable\n with prefix http://identifiers.org/massive/\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=83574f41458a4b259621d5c32a4d82f9\nrank: 1000\nis_a: study_identifiers\nmixins:\n- massive_identifiers\nmultivalued: true\nalias: massive_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: '^MASSIVE:'\n\nURI: nmdc:material_input
"},{"location":"material_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity yes ReactionActivity no"},{"location":"material_input/#properties","title":"Properties","text":"name: material_input\ntitle: material input\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_input\ndomain_of:\n- DissolvingActivity\n- ReactionActivity\nrange: MaterialSample\n\nURI: nmdc:material_output
"},{"location":"material_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DissolvingActivity yes MaterialSamplingActivity yes ReactionActivity no"},{"location":"material_output/#properties","title":"Properties","text":"name: material_output\ntitle: material output\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_output\ndomain_of:\n- DissolvingActivity\n- MaterialSamplingActivity\n- ReactionActivity\nrange: MaterialSample\n\nURI: nmdc:material_sample_set
"},{"location":"material_sample_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_sample_set/#properties","title":"Properties","text":"Range: MaterialSample
Multivalued: True
name: material_sample_set\ntitle: material sample set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: material_sample_set\ndomain_of:\n- Database\nrange: MaterialSample\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:material_sampling_activity_set
"},{"location":"material_sampling_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"material_sampling_activity_set/#properties","title":"Properties","text":"Range: MaterialSamplingActivity
Multivalued: True
name: material_sampling_activity_set\ntitle: material sampling activity set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: material_sampling_activity_set\ndomain_of:\n- Database\nrange: MaterialSamplingActivity\ninlined: true\ninlined_as_list: true\n\nThe maximum amount of people allowed in the indoor environment
URI: MIXS:0000229
"},{"location":"max_occup/#inheritance","title":"Inheritance","text":"name: max_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nmultivalued: false\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMD5 checksum of file (pre-compressed)
URI: nmdc:md5_checksum
"},{"location":"md5_checksum/#inheritance","title":"Inheritance","text":"name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\nMeasurement of mean friction velocity
URI: MIXS:0000498
"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nmultivalued: false\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of mean peak friction velocity
URI: MIXS:0000502
"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_peak_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nmultivalued: false\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nmechanical structure: a moving structure
URI: MIXS:0000815
"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":"name: mech_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nmultivalued: false\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\n\nInformation about any mechanical damage exerted on the plant; can include multiple damages and sites
URI: MIXS:0001052
"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mechanical_damage\nannotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nmultivalued: true\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:members_id
"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":"name: members_id\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\n\nthe specific metabolite identifier
URI: nmdc:metabolite_quantified
"},{"location":"metabolite_quantified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteQuantification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_quantified/#properties","title":"Properties","text":"name: metabolite_quantified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_quantified\ndomain_of:\n- MetaboliteQuantification\nrange: ChemicalEntity\n\nThis property links a database object to the set of metabolomics analysis activities.
URI: nmdc:metabolomics_analysis_activity_set
"},{"location":"metabolomics_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: MetabolomicsAnalysisActivity
Multivalued: True
name: metabolomics_analysis_activity_set\ndescription: This property links a database object to the set of metabolomics analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metabolomics_analysis_activity_set\ndomain_of:\n- Database\nrange: MetabolomicsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metagenome annotation activities.
URI: nmdc:metagenome_annotation_activity_set
"},{"location":"metagenome_annotation_activity_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeAnnotationActivity
Multivalued: True
name: metagenome_annotation_activity_set\ndescription: This property links a database object to the set of metagenome annotation\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_annotation_activity_set\ndomain_of:\n- Database\nrange: MetagenomeAnnotationActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:metagenome_annotation_id
"},{"location":"metagenome_annotation_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":"name: metagenome_annotation_id\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: WorkflowExecutionActivity\n\nURI: nmdc:metagenome_assembly_parameter
"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":"name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\nThis property links a database object to the set of metagenome assembly activities.
URI: nmdc:metagenome_assembly_set
"},{"location":"metagenome_assembly_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeAssembly
Multivalued: True
name: metagenome_assembly_set\ndescription: This property links a database object to the set of metagenome assembly\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_assembly_set\ndomain_of:\n- Database\nrange: MetagenomeAssembly\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metagenome sequencing activities.
URI: nmdc:metagenome_sequencing_activity_set
"},{"location":"metagenome_sequencing_activity_set/#inheritance","title":"Inheritance","text":"Range: MetagenomeSequencingActivity
Multivalued: True
name: metagenome_sequencing_activity_set\ndescription: This property links a database object to the set of metagenome sequencing\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metagenome_sequencing_activity_set\ndomain_of:\n- Database\nrange: MetagenomeSequencingActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metaproteomics analysis activities.
URI: nmdc:metaproteomics_analysis_activity_set
"},{"location":"metaproteomics_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: MetaproteomicsAnalysisActivity
Multivalued: True
name: metaproteomics_analysis_activity_set\ndescription: This property links a database object to the set of metaproteomics analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metaproteomics_analysis_activity_set\ndomain_of:\n- Database\nrange: MetaproteomicsAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of metatranscriptome analysis activities.
URI: nmdc:metatranscriptome_activity_set
"},{"location":"metatranscriptome_activity_set/#inheritance","title":"Inheritance","text":"Range: MetatranscriptomeActivity
Multivalued: True
name: metatranscriptome_activity_set\ndescription: This property links a database object to the set of metatranscriptome\n analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: metatranscriptome_activity_set\ndomain_of:\n- Database\nrange: MetatranscriptomeActivity\ninlined: true\ninlined_as_list: true\n\nMethane (gas) amount or concentration at the time of sampling
URI: MIXS:0000101
"},{"location":"methane/#inheritance","title":"Inheritance","text":"name: methane\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nmultivalued: false\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:mgnify_analysis_identifiers
"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nmultivalued: true\nalias: mgnify_analysis_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:mgnify_identifiers
"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\nidentifiers for corresponding project in MGnify
URI: nmdc:mgnify_project_identifiers
"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^mgnify.proj:[A-Z]+[0-9]+$
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nmultivalued: true\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\nReference or method used in determining microbial biomass carbon
URI: nmdc:micro_biomass_c_meth
"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nReference or method used in determining microbial biomass
URI: MIXS:0000339
"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":"name: micro_biomass_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nmultivalued: false\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining microbial biomass nitrogen
URI: nmdc:micro_biomass_n_meth
"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":"name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units
URI: MIXS:0000650
"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":"name: microbial_biomass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer. If you keep this, you would need to have correction\n factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nmultivalued: false\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_c
"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":"name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_n
"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":"name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nsmallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool
URI: nmdc:min_q_value
"},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":"name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n MSGFPlus tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\nInformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens
URI: MIXS:0000570
"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mineral_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple mineral\n nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nmultivalued: true\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nAny other measurement performed or parameter collected, that is not listed here
URI: MIXS:0000752
"},{"location":"misc_param/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: misc_param\nannotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nmultivalued: true\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe last date on which the database information was modified.
URI: nmdc:mod_date
"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"mod_date/#properties","title":"Properties","text":"name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: string\n\nConcentration of n-alkanes; can include multiple n-alkanes
URI: MIXS:0000503
"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: n_alkanes\nannotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nmultivalued: true\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\n\nA human readable label for an entity
URI: nmdc:name
"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Protocol no QualityControlReport no NamedThing a databased entity or concept/class no PersonValue An attribute value representing a person yes Activity a provence-generating activity no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CollectingBiosamplesFromSite no DataObject An object that primarily consists of symbols that represent information yes Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... yes BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no MaterialEntity no ProcessedSample no AnalyticalSample no Site no PlannedProcess no OntologyClass no EnvironmentalMaterialTerm no Instrument A material entity that is designed to perform a function in a scientific inve... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no GeneProduct A molecule encoded by a gene that has an evolved function no MaterialSample no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no Reaction An individual biochemical transformation carried out by a functional unit of ... no OrthologyGroup A set of genes or gene products in which all members are orthologous no"},{"location":"name/#properties","title":"Properties","text":"name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- Protocol\n- QualityControlReport\n- NamedThing\n- PersonValue\n- Activity\nrange: string\n\nURI: nmdc:ncbi_project_name
"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":"name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- OmicsProcessing\nrange: string\n\nURI: nmdc:ncbi_taxonomy_name
"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":"name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:neon_biosample_identifiers
"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nmultivalued: true\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:neon_deims_sdr_link
"},{"location":"neon_deims_sdr_link/#properties","title":"Properties","text":"name: neon_deims_sdr_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_deims_sdr_link\nrange: string\n\nURI: nmdc:neon_eco_type
"},{"location":"neon_eco_type/#properties","title":"Properties","text":"name: neon_eco_type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_eco_type\nrange: string\n\nidentifiers for entities according to NEON
URI: nmdc:neon_identifiers
"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\nURI: nmdc:neon_soil_type
"},{"location":"neon_soil_type/#properties","title":"Properties","text":"name: neon_soil_type\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: neon_soil_type\nrange: string\n\nURI: nmdc:neon_study_identifiers
"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nmultivalued: true\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nConcentration of nitrate in the sample
URI: MIXS:0000425
"},{"location":"nitrate/#inheritance","title":"Inheritance","text":"name: nitrate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nmultivalued: false\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrate nitrogen in the sample
URI: nmdc:nitrate_nitrogen
"},{"location":"nitrate_nitrogen/#inheritance","title":"Inheritance","text":"name: nitrate_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nis_a: attribute\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite in the sample
URI: MIXS:0000426
"},{"location":"nitrite/#inheritance","title":"Inheritance","text":"name: nitrite\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nmultivalued: false\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite nitrogen in the sample
URI: nmdc:nitrite_nitrogen
"},{"location":"nitrite_nitrogen/#inheritance","title":"Inheritance","text":"name: nitrite_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nis_a: attribute\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrogen (total)
URI: MIXS:0000504
"},{"location":"nitro/#inheritance","title":"Inheritance","text":"name: nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nmultivalued: false\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThis property links a database object to the set of natural organic matter (NOM) analysis activities.
URI: nmdc:nom_analysis_activity_set
"},{"location":"nom_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: NomAnalysisActivity
Multivalued: True
name: nom_analysis_activity_set\ndescription: This property links a database object to the set of natural organic matter\n (NOM) analysis activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: nom_analysis_activity_set\ndomain_of:\n- Database\nrange: NomAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nAmount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;
URI: nmdc:non_microb_biomass
"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":"name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nReference or method used in determining biomass
URI: nmdc:non_microb_biomass_method
"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":"name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nInformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens
URI: MIXS:0000571
"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: non_min_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nmultivalued: true\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\n\nfrom study class
URI: nmdc:notes
"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":"name: notes\ndescription: from study class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
URI: MIXS:0000038
"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":"name: nucl_acid_amp\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nmultivalued: false\nalias: nucl_acid_amp\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
URI: MIXS:0000037
"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":"name: nucl_acid_ext\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the material separation to recover the nucleic acid\n fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nmultivalued: false\nalias: nucl_acid_ext\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:nucleic_acid_concentration
"},{"location":"nucleic_acid_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no"},{"location":"nucleic_acid_concentration/#properties","title":"Properties","text":"name: nucleic_acid_concentration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: nucleic_acid_concentration\ndomain_of:\n- ProcessedSample\nrange: InstrumentValue\n\nURI: nmdc:nucleic_acid_sequence_source_field
"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":"name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:num_16s
"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":"name: num_16s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:num_23s
"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":"name: num_23s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:num_5s
"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":"name: num_5s\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\n\nThe sequence count number of input reads aligned to assembled contigs.
URI: nmdc:num_aligned_reads
"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":"name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sequence count number of input reads for assembly.
URI: nmdc:num_input_reads
"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":"name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nURI: nmdc:num_t_rna
"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":"name: num_t_rna\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\n\nURI: nmdc:number_of_contig
"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":"name: number_of_contig\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\n\nThe number of pets residing in the sampled space
URI: MIXS:0000231
"},{"location":"number_pets/#inheritance","title":"Inheritance","text":"name: number_pets\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nmultivalued: false\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of plant(s) in the sampling space
URI: MIXS:0000230
"},{"location":"number_plants/#inheritance","title":"Inheritance","text":"name: number_plants\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nmultivalued: false\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe number of individuals currently occupying in the sampling location
URI: MIXS:0000232
"},{"location":"number_resident/#inheritance","title":"Inheritance","text":"name: number_resident\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nmultivalued: false\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nApplies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types
URI: nmdc:object_set
"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database activity_set This property links a database object to the set of workflow activities WorkflowExecutionActivity Database mags_activity_set This property links a database object to the set of MAGs analysis activities MagsAnalysisActivity Database metabolomics_analysis_activity_set This property links a database object to the set of metabolomics analysis act... MetabolomicsAnalysisActivity Database metaproteomics_analysis_activity_set This property links a database object to the set of metaproteomics analysis a... MetaproteomicsAnalysisActivity Database metagenome_annotation_activity_set This property links a database object to the set of metagenome annotation act... MetagenomeAnnotationActivity Database metagenome_assembly_set This property links a database object to the set of metagenome assembly activ... MetagenomeAssembly Database metagenome_sequencing_activity_set This property links a database object to the set of metagenome sequencing act... MetagenomeSequencingActivity Database metatranscriptome_activity_set This property links a database object to the set of metatranscriptome analysi... MetatranscriptomeActivity Database read_qc_analysis_activity_set This property links a database object to the set of read QC analysis activiti... ReadQcAnalysisActivity Database read_based_taxonomy_analysis_activity_set This property links a database object to the set of read based analysis activ... ReadBasedTaxonomyAnalysisActivity Database nom_analysis_activity_set This property links a database object to the set of natural organic matter (N... NomAnalysisActivity Database omics_processing_set This property links a database object to the set of omics processings within ... OmicsProcessing Database pooling_set Pooling Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database extraction_set This property links a database object to the set of extractions within it Extraction Database library_preparation_set This property links a database object to the set of DNA extractions within it LibraryPreparation Database"},{"location":"object_set/#properties","title":"Properties","text":"Range: String
Multivalued: True
Mixin: True
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n This is necessary in a json document to provide context for a list, and to allow\n for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\ndomain: Database\nmultivalued: true\nalias: object_set\nrange: string\ninlined_as_list: true\n\nThe scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.
URI: nmdc:objective
"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":"name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nmultivalued: false\nalias: objective\ndomain_of:\n- Study\nrange: string\n\nAverage number of occupants at time of sampling per square footage
URI: MIXS:0000217
"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":"name: occup_density_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nmultivalued: false\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of documentation of occupancy
URI: MIXS:0000816
"},{"location":"occup_document/#inheritance","title":"Inheritance","text":"name: occup_document\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nmultivalued: false\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\n\nNumber of occupants present at time of sample within the given space
URI: MIXS:0000772
"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":"name: occup_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nmultivalued: false\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:omics_processing_identifiers
"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: omics_processing_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of omics processings within it.
URI: nmdc:omics_processing_set
"},{"location":"omics_processing_set/#inheritance","title":"Inheritance","text":"Range: OmicsProcessing
Multivalued: True
name: omics_processing_set\ndescription: This property links a database object to the set of omics processings\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: omics_processing_set\ndomain_of:\n- Database\nrange: OmicsProcessing\ninlined: true\ninlined_as_list: true\n\nThe type of omics data
URI: nmdc:omics_type
"},{"location":"omics_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"omics_type/#properties","title":"Properties","text":"name: omics_type\ndescription: The type of omics data\nnotes:\n- was the range string at one point? the values in MongoDB don't look like NMDC classes\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: omics_type\ndomain_of:\n- OmicsProcessing\nrange: ControlledTermValue\n\nThe ORCID of a person.
URI: nmdc:orcid
"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":"name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: PersonValue\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\nConcentration of organic carbon
URI: MIXS:0000508
"},{"location":"org_carb/#inheritance","title":"Inheritance","text":"name: org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nmultivalued: false\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nIf qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)
URI: MIXS:0000099
"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":"name: org_count_qpcr_info\nannotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nmultivalued: false\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of organic matter
URI: MIXS:0000204
"},{"location":"org_matter/#inheritance","title":"Inheritance","text":"name: org_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nmultivalued: false\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of organic nitrogen
URI: MIXS:0000205
"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":"name: org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nmultivalued: false\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod used for obtaining organic nitrogen
URI: nmdc:org_nitro_method
"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":"name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nConcentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.
URI: MIXS:0000665
"},{"location":"org_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: org_particles\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nmultivalued: true\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
URI: MIXS:0000103
"},{"location":"organism_count/#inheritance","title":"Inheritance","text":"Range: QuantityValue
Multivalued: True
name: organism_count\nannotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n or area of sample, should include name of organism followed by count. The method\n that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nmultivalued: true\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOther treatments applied to your samples that are not applicable to the provided fields
URI: nmdc:other_treatment
"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":"Range: String
Recommended: True
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n provided fields\ntitle: other treatments\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nAfter QC analysis nucleotide base count number.
URI: nmdc:output_base_count
"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":"name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nTODO
URI: nmdc:output_read_bases
"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":"name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nAfter QC analysis sequence count number.
URI: nmdc:output_read_count
"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":"name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysisActivity\nrange: float\n\nDepth of the original oil water contact (OWC) zone (average) (m TVDSS)
URI: MIXS:0000405
"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":"name: owc_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nmultivalued: false\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOxygenation status of sample
URI: MIXS:0000753
"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":"name: oxy_stat_samp\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nmultivalued: false\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\n\nOxygen (gas) amount or concentration at the time of sampling
URI: MIXS:0000104
"},{"location":"oxygen/#inheritance","title":"Inheritance","text":"name: oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nmultivalued: false\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nLinks a resource to another resource that either logically or physically includes it.
URI: dcterms:isPartOf
"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment yes Study A study summarizes the overall goal of a research initiative and outlines the... yes OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"part_of/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\ndomain: NamedThing\nslot_uri: dcterms:isPartOf\nmultivalued: true\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Biosample\n- Study\n- OmicsProcessing\n- WorkflowExecutionActivity\nrange: NamedThing\n\nConcentration of particulate organic carbon
URI: MIXS:0000515
"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":"name: part_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nmultivalued: false\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of particulate organic nitrogen
URI: MIXS:0000719
"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":"name: part_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nmultivalued: false\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nParticles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values
URI: MIXS:0000206
"},{"location":"particle_class/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: particle_class\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nmultivalued: true\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\n\nDescription of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
URI: MIXS:0000049
"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":"name: pcr_cond\nannotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nmultivalued: false\nalias: pcr_cond\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:pcr_cycles
"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":"name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\nPCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
URI: MIXS:0000046
"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":"name: pcr_primers\nannotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n locus or subfragment. This field should contain all the primers used for a single\n PCR reaction if multiple forward or reverse primers are present in a single PCR\n reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nmultivalued: false\nalias: pcr_primers\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nURI: nmdc:peptide_sequence
"},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":"name: peptide_sequence\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\ncount of peptide sequences grouped to the best_protein
URI: nmdc:peptide_sequence_count
"},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":"name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nsum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file
URI: nmdc:peptide_spectral_count
"},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":"name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:peptide_sum_masic_abundance
"},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":"name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\nMeasure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability(earth_sciences))_
URI: MIXS:0000404
"},{"location":"permeability/#inheritance","title":"Inheritance","text":"name: permeability\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nmultivalued: false\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\n\nType of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
URI: MIXS:0000754
"},{"location":"perturbation/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: perturbation\nannotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time of the\n entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nmultivalued: true\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens
URI: MIXS:0000573
"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pesticide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of insecticides; should include\n the name of pesticide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nmultivalued: true\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of petroleum hydrocarbon
URI: MIXS:0000516
"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":"name: petroleum_hydrocarb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nmultivalued: false\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nPh measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
URI: MIXS:0001001
"},{"location":"ph/#inheritance","title":"Inheritance","text":"name: ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nmultivalued: false\nalias: ph\ndomain_of:\n- Biosample\nrange: double\n\nReference or method used in determining ph
URI: MIXS:0001106
"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":"name: ph_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nmultivalued: false\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen
URI: MIXS:0001056
"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: ph_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n of ph of the growth media, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nmultivalued: true\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of phaeopigments; can include multiple phaeopigments
URI: MIXS:0000180
"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phaeopigments\nannotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nmultivalued: true\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.
URI: nmdc:phase
"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
Maximum Value: 2
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\nConcentration of phosphate
URI: MIXS:0000505
"},{"location":"phosphate/#inheritance","title":"Inheritance","text":"name: phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nmultivalued: false\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of phospholipid fatty acids; can include multiple values
URI: MIXS:0000181
"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phosplipid_fatt_acid\nannotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nmultivalued: true\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of photon flux
URI: MIXS:0000725
"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":"name: photon_flux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nmultivalued: false\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSpecification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
URI: MIXS:0001057
"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":"name: plant_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n liquid culture medium. Recommended value is a specific value from EO:plant growth\n medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nmultivalued: false\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nSubstance produced by the plant, where the sample was obtained from
URI: MIXS:0001058
"},{"location":"plant_product/#inheritance","title":"Inheritance","text":"name: plant_product\nannotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nmultivalued: false\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\n\nSex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.
URI: MIXS:0001059
"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":"name: plant_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nmultivalued: false\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\n\nName of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.
URI: MIXS:0001060
"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":"name: plant_struc\nannotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nmultivalued: false\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nPollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
URI: MIXS:0000107
"},{"location":"pollutants/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pollutants\nannotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n sampling; can report multiple pollutants by entering numeric values preceded by\n name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nmultivalued: true\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\n\nIndicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
URI: MIXS:0000325
"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":"name: pool_dna_extracts\nannotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nmultivalued: false\nalias: pool_dna_extracts\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:pooling_set
"},{"location":"pooling_set/#inheritance","title":"Inheritance","text":"Range: Pooling
Multivalued: True
name: pooling_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: pooling_set\ndomain_of:\n- Database\nrange: Pooling\ninlined: true\ninlined_as_list: true\n\nPorosity of deposited sediment is volume of voids divided by the total volume of sample
URI: MIXS:0000211
"},{"location":"porosity/#inheritance","title":"Inheritance","text":"name: porosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nmultivalued: false\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of potassium in the sample
URI: MIXS:0000430
"},{"location":"potassium/#inheritance","title":"Inheritance","text":"name: potassium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nmultivalued: false\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTemperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)
URI: MIXS:0000127
"},{"location":"pour_point/#inheritance","title":"Inheritance","text":"name: pour_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nmultivalued: false\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe process of pre-treatment removes materials that can be easily collected from the raw wastewater
URI: MIXS:0000348
"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":"name: pre_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nmultivalued: false\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nAll metadata gathered and stored by the NMDC community must validate against the nmdc-schema.
"},{"location":"prefixes_curies_ids_mappings_etc/#the-nmdc-schema-is-expressed-in-the-linkml-schema-language","title":"The nmdc-schema is expressed in the LinkML schema language.","text":"LinkML uses structures like classes, slots (for relationships and properties), types and enumerations. People with object-oriented programming experience might find this familiar.
"},{"location":"prefixes_curies_ids_mappings_etc/#the-name-linkml-indicates-that-its-a-modeling-language-for-linked-data","title":"The name \"LinkML\" indicates that it's' a modeling language for linked data.","text":"LinkML schemas generally make good use of terminology from external resources, especially ontologies, especially those from the OBO Foundry. In return, LinkML schema elements and the corresponding data should be interoperable with other ontologies and semantic databases.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-element-identifiers-in-the-schema-with-uris-and-curies","title":"Asserting element identifiers in the schema with URIs and CURIEs","text":"One consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.
Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the nmdc-schema","text":"As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.
Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.
Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.
When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.
"},{"location":"prefixes_curies_ids_mappings_etc/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.
A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs.
pooling_set:\n - id: pooling:1\n inputs:\n - biosample:1\n - biosample:2\n - biosample:3\n - id: pooling:2\n inputs:\n - biosample:4\n - biosample:5\n - biosample:6\nHere we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.
In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.
Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.
biosample_set:\n - id: biosample:1\n gold_biosample_identifiers:\n - gold:1\n - gold:2\nIn this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.
"},{"location":"prefixes_curies_ids_mappings_etc/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )
All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.
Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.
Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.
If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'
make gen-project)default_curi_maps any more--emsl-biosample-uuid-replacement in anyuri-strings-to-iris--salvage-prefix added by migration-recursionpatterns and id_prefixeswarning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)
warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)
"},{"location":"prefixes_curies_ids_mappings_etc/#unresolved","title":"unresolved","text":"make better use of id prefixes?
todo what reference ontologies do we want to include in a graph database?
could federate uniprot
gen-prefix-map
emits JSON content into a file with teh .yaml extension by default
doesn't look like all the emit_prefixes are making it into the OWL output
two graphdb endpoints: http://3.236.215.220:7200/sparql (switch to port 80) and https://graphdb-dev.microbiomedata.org/
make squeaky-clean does not include mixs-yaml-clean, so that mixs.yaml isn't unnecessarily regeneratedThe type and number of animals or insects present in the sampling space.
URI: MIXS:0000819
"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^(cat|dog|rodent|snake|other);\\d+$
name: pres_animal_insect\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nmultivalued: false\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\nPressure to which the sample is subject to, in atmospheres
URI: MIXS:0000412
"},{"location":"pressure/#inheritance","title":"Inheritance","text":"name: pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nmultivalued: false\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining previous land use and dates
URI: MIXS:0000316
"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":"name: prev_land_use_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nmultivalued: false\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\n\nPrevious land use and dates
URI: MIXS:0000315
"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":"name: previous_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nmultivalued: false\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of primary production, generally measured as isotope uptake
URI: MIXS:0000728
"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":"name: primary_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nmultivalued: false\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed
URI: MIXS:0000349
"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":"name: primary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nmultivalued: false\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nPrincipal Investigator who led the study and/or generated the dataset.
URI: nmdc:principal_investigator
"},{"location":"principal_investigator/#inheritance","title":"Inheritance","text":"name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nis_a: attribute\nalias: principal_investigator\ndomain_of:\n- Study\n- OmicsProcessing\nrange: PersonValue\n\nThis property links a database object to the set of processed samples within it.
URI: nmdc:processed_sample_set
"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":"Range: ProcessedSample
Multivalued: True
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\ninlined: true\ninlined_as_list: true\n\nThe organization that processed the sample.
URI: nmdc:processing_institution
"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"processing_institution/#properties","title":"Properties","text":"name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- Extraction\n- LibraryPreparation\n- OmicsProcessing\nrange: processing_institution_enum\n\nOil and/or gas production rates per well (e.g. 524 m3 / day)
URI: MIXS:0000452
"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":"name: prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nmultivalued: false\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nDate of field's first production
URI: MIXS:0001008
"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":"name: prod_start_date\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nmultivalued: false\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\n\nA url that points to an image of a person.
URI: nmdc:profile_image_url
"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":"name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: PersonValue\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\nCross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
URI: MIXS:0001084
"},{"location":"profile_position/#inheritance","title":"Inheritance","text":"name: profile_position\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nmultivalued: false\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\n\nProposal IDs or names associated with dataset
URI: nmdc:project_id
"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nURI: nmdc:proport_woa_temperature
"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":"name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:proposal_dna
"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:proposal_rna
"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nsum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file
URI: nmdc:protein_spectral_count
"},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":"name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n a given LC-MS/MS data file\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:protein_sum_masic_abundance
"},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":"name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the best protein from a given LC-MS/MS data file using the MASIC tool\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nURI: nmdc:protocol_link
"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no PlannedProcess no Pooling physical combination of several instances of like material no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"protocol_link/#properties","title":"Properties","text":"name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- Extraction\n- PlannedProcess\nrange: Protocol\n\nOne or more DOIs that links a study, or similar entity, to a publication.
URI: nmdc:publication_dois
"},{"location":"publication_dois/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: publication_dois\ndescription: One or more DOIs that links a study, or similar entity, to a publication.\nexamples:\n- value: doi:10.1126/science.1058040\n description: publication_dois link to a prose document, preferably a peer-reviewed\n journal article. Should not be used to link to datasets or administrative information\n like funding requests or awards\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: dois\nmultivalued: true\nalias: publication_dois\ndomain_of:\n- Study\nrange: uriorcurie\npattern: ^doi:10.\\d{2,9}/.*$\n\nA list of publications that are associated with the entity. The publications SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.
URI: nmdc:publications
"},{"location":"publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"publications/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: publications\ndescription: A list of publications that are associated with the entity. The publications\n SHOULD be given using an identifier, such as a DOI or Pubmed ID, if possible.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: publications\ndomain_of:\n- Study\nrange: string\n\nThe quadrant position of the sampling room within the building
URI: MIXS:0000820
"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":"name: quad_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nmultivalued: false\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\n\nURI: nmdc:quality_control_report
"},{"location":"quality_control_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"quality_control_report/#properties","title":"Properties","text":"name: quality_control_report\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: quality_control_report\ndomain_of:\n- Extraction\nrange: QualityControlReport\n\nInformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens
URI: MIXS:0000575
"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: radiation_regm\nannotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n to a particular radiation regimen; should include the radiation type, amount or\n intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nmultivalued: true\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000576
"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: rainfall_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to a given amount of\n rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nmultivalued: true\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:reaction_activity_set
"},{"location":"reaction_activity_set/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"reaction_activity_set/#properties","title":"Properties","text":"Range: ReactionActivity
Multivalued: True
name: reaction_activity_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: reaction_activity_set\ndomain_of:\n- Database\nrange: ReactionActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:reaction_aided_by
"},{"location":"reaction_aided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity no"},{"location":"reaction_aided_by/#properties","title":"Properties","text":"name: reaction_aided_by\ntitle: reaction aided by\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shaker\nrank: 1000\nalias: reaction_aided_by\ndomain_of:\n- ReactionActivity\nrange: LabDevice\ninlined: true\n\nURI: nmdc:reaction_temperature
"},{"location":"reaction_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity no"},{"location":"reaction_temperature/#properties","title":"Properties","text":"name: reaction_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: reaction_temperature\ndomain_of:\n- ReactionActivity\nrange: string\n\nURI: nmdc:reaction_time
"},{"location":"reaction_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionActivity yes"},{"location":"reaction_time/#properties","title":"Properties","text":"name: reaction_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: reaction_time\ndomain_of:\n- ReactionActivity\nrange: QuantityValue\ninlined: true\n\nAnaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage
URI: MIXS:0000350
"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":"name: reactor_type\nannotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nmultivalued: false\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nThis property links a database object to the set of read based analysis activities.
URI: nmdc:read_based_taxonomy_analysis_activity_set
"},{"location":"read_based_taxonomy_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: ReadBasedTaxonomyAnalysisActivity
Multivalued: True
name: read_based_taxonomy_analysis_activity_set\ndescription: This property links a database object to the set of read based analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: read_based_taxonomy_analysis_activity_set\ndomain_of:\n- Database\nrange: ReadBasedTaxonomyAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of read QC analysis activities.
URI: nmdc:read_qc_analysis_activity_set
"},{"location":"read_qc_analysis_activity_set/#inheritance","title":"Inheritance","text":"Range: ReadQcAnalysisActivity
Multivalued: True
name: read_qc_analysis_activity_set\ndescription: This property links a database object to the set of read QC analysis\n activities.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: read_qc_analysis_activity_set\ndomain_of:\n- Database\nrange: ReadQcAnalysisActivity\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:read_qc_analysis_statistic
"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":"name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\nRedox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
URI: MIXS:0000182
"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":"name: redox_potential\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nmultivalued: false\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nPartial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
URI: MIXS:0000121
"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":"name: rel_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nmultivalued: false\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe recorded outside relative humidity value at the time of sampling
URI: MIXS:0000188
"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":"name: rel_humidity_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nmultivalued: false\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe sampling location within the train car
URI: MIXS:0000821
"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":"name: rel_samp_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nmultivalued: false\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\n\nIdentifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.
URI: nmdc:related_identifiers
"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":"name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\nURI: nmdc:relevant_protocols
"},{"location":"relevant_protocols/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"relevant_protocols/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: relevant_protocols\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: relevant_protocols\ndomain_of:\n- Study\nrange: string\n\nIf sending biological replicates, indicate the rep number here.
URI: nmdc:replicate_number
"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":"Range: String
Recommended: True
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nName of the reservoir (e.g. Carapebus)
URI: MIXS:0000303
"},{"location":"reservoir/#inheritance","title":"Inheritance","text":"name: reservoir\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nmultivalued: false\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000134
"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":"name: resins_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nmultivalued: false\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:right_participants
"},{"location":"right_participants/#inheritance","title":"Inheritance","text":"Range: ReactionParticipant
Multivalued: True
name: right_participants\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_participants\nmultivalued: true\nalias: right_participants\ndomain_of:\n- Reaction\nrange: ReactionParticipant\n\n260/280 measurement of RNA sample purity
URI: nmdc:rna_absorb1
"},{"location":"rna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n260/230 measurement of RNA sample purity
URI: nmdc:rna_absorb2
"},{"location":"rna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\nProvide information on the site your RNA sample was collected from
URI: nmdc:rna_collect_site
"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_concentration
"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nTube or plate (96-well)
URI: nmdc:rna_cont_type
"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:rna_cont_well
"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:rna_container_id
"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:rna_isolate_meth
"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:rna_organisms
"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_project_contact
"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_samp_id
"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nSolution in which the RNA sample has been suspended
URI: nmdc:rna_sample_format
"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":"Range: RnaSampleFormatEnum
Recommended: True
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: rna_sample_format_enum\nrecommended: true\n\nGive the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:rna_sample_name
"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nURI: nmdc:rna_seq_project
"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_name
"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_pi
"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_volume
"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nThe rate at which outside air replaces indoor air in a given space
URI: MIXS:0000169
"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":"name: room_air_exch_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nmultivalued: false\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure
URI: MIXS:0000233
"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":"name: room_architec_elem\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nmultivalued: false\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\n\nThe condition of the room at the time of sampling
URI: MIXS:0000822
"},{"location":"room_condt/#inheritance","title":"Inheritance","text":"name: room_condt\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nmultivalued: false\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\n\nList of rooms connected to the sampling room by a doorway
URI: MIXS:0000826
"},{"location":"room_connected/#inheritance","title":"Inheritance","text":"name: room_connected\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nmultivalued: false\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\n\nThe total count of rooms in the built structure including all room types
URI: MIXS:0000234
"},{"location":"room_count/#inheritance","title":"Inheritance","text":"name: room_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nmultivalued: false\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe length, width and height of sampling room
URI: MIXS:0000192
"},{"location":"room_dim/#inheritance","title":"Inheritance","text":"name: room_dim\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nmultivalued: false\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\n\nDistance between doors (meters) in the hallway between the sampling room and adjacent rooms
URI: MIXS:0000193
"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":"name: room_door_dist\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nmultivalued: false\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) sharing a door with the sampling room
URI: MIXS:0000242
"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":"name: room_door_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nmultivalued: false\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) located in the same hallway as sampling room
URI: MIXS:0000238
"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":"name: room_hallway\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nmultivalued: false\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe position of the room within the building
URI: MIXS:0000823
"},{"location":"room_loc/#inheritance","title":"Inheritance","text":"name: room_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nmultivalued: false\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\n\nThe history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
URI: MIXS:0000235
"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":"name: room_moist_dam_hist\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nmultivalued: false\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\n\nThe net floor area of sampling room. Net area excludes wall thicknesses
URI: MIXS:0000194
"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":"name: room_net_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nmultivalued: false\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\n\nCount of room occupancy at time of sampling
URI: MIXS:0000236
"},{"location":"room_occup/#inheritance","title":"Inheritance","text":"name: room_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nmultivalued: false\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe horizontal sampling position in the room relative to architectural elements
URI: MIXS:0000824
"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":"name: room_samp_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nmultivalued: false\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\n\nThe main purpose or activity of the sampling room. A room is any distinguishable space within a structure
URI: MIXS:0000825
"},{"location":"room_type/#inheritance","title":"Inheritance","text":"name: room_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nmultivalued: false\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\n\nVolume of sampling room
URI: MIXS:0000195
"},{"location":"room_vol/#inheritance","title":"Inheritance","text":"name: room_vol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nmultivalued: false\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\n\nList of room(s) (room number, room name) sharing a wall with the sampling room
URI: MIXS:0000243
"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":"name: room_wall_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nmultivalued: false\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\n\nNumber of windows in the room
URI: MIXS:0000237
"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":"name: room_window_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nmultivalued: false\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\n\nRelevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.
URI: MIXS:0001061
"},{"location":"root_cond/#inheritance","title":"Inheritance","text":"name: root_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nmultivalued: false\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nSource of organic carbon in the culture rooting medium; e.g. sucrose.
URI: MIXS:0000577
"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":"name: root_med_carbon\nannotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nmultivalued: false\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).
URI: MIXS:0000578
"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":"name: root_med_macronutr\nannotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nmultivalued: false\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\n\nMeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).
URI: MIXS:0000579
"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":"name: root_med_micronutr\nannotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nmultivalued: false\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\n\npH measurement of the culture rooting medium; e.g. 5.5.
URI: MIXS:0001062
"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":"name: root_med_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nmultivalued: false\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nGrowth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.
URI: MIXS:0000581
"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":"name: root_med_regl\nannotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nmultivalued: false\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\n\nSpecification of the solidifying agent in the culture rooting medium; e.g. agar.
URI: MIXS:0001063
"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":"name: root_med_solid\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nmultivalued: false\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\n\nOrganic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).
URI: MIXS:0000580
"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":"name: root_med_suppl\nannotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nmultivalued: false\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.
URI: MIXS:0000183
"},{"location":"salinity/#inheritance","title":"Inheritance","text":"name: salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n While salinity can be measured by a complete chemical analysis, this method is difficult\n and time consuming. More often, it is instead derived from the conductivity measurement.\n This is known as practical salinity. These derivations compare the specific conductance\n of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nmultivalued: false\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCategorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline
URI: nmdc:salinity_category
"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":"name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining salinity
URI: MIXS:0000341
"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":"name: salinity_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nmultivalued: false\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens
URI: MIXS:0000582
"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: salt_regm\nannotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n and soil growth media; should include the name of salt, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nmultivalued: true\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nReason for the sample
URI: MIXS:0000860
"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":"name: samp_capt_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nmultivalued: false\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\n\nThe device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
URI: MIXS:0000002
"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":"name: samp_collec_device\nannotations:\n expected_value:\n tag: expected_value\n value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nmultivalued: false\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\n\nThe method employed for collecting the sample.
URI: MIXS:0001225
"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":"name: samp_collec_method\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nmultivalued: false\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\n\nSampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001015
"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":"name: samp_collect_point\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry in\n \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nmultivalued: false\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\n\nStage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.
URI: MIXS:0000249
"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":"name: samp_dis_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nmultivalued: false\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\n\nThe floor of the building, where the sampling room is located
URI: MIXS:0000828
"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":"name: samp_floor\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nmultivalued: false\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\n\nMetal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays
URI: MIXS:0000136
"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":"name: samp_loc_corr_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short term\n rates and for that reason they are preferred during reporting. In the case of suspected\n MIC, corrosion rate measurements at the time of sampling might provide insights\n into the involvement of certain microbial community members in MIC as well as potential\n microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nmultivalued: false\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\n\nA brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.
URI: MIXS:0000016
"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":"name: samp_mat_process\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A brief description of any processing applied to the sample during or\n after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nmultivalued: false\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\n\nIn non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000413
"},{"location":"samp_md/#inheritance","title":"Inheritance","text":"name: samp_md\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n MD is the length of trajectory of the borehole measured from the same reference\n or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nmultivalued: false\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nA local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.
URI: MIXS:0001107
"},{"location":"samp_name/#inheritance","title":"Inheritance","text":"name: samp_name\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A local identifier or name that for the material sample used for extracting\n nucleic acids, and subsequent sequencing. It can refer either to the original material\n collected or to any derived sub-samples. It can have any format, but we suggest\n that you make it concise, unique and consistent within your lab, and as informative\n as possible. INSDC requires every sample name from a single Submitter to be unique.\n Use of a globally unique identifier for the field source_mat_id is recommended in\n addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nmultivalued: false\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\n\nPreservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
URI: MIXS:0000463
"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":"name: samp_preserv\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nmultivalued: false\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\n\nSampling room number. This ID should be consistent with the designations on the building floor plans
URI: MIXS:0000244
"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":"name: samp_room_id\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nmultivalued: false\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
URI: MIXS:0000001
"},{"location":"samp_size/#inheritance","title":"Inheritance","text":"name: samp_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nmultivalued: false\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMethod by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.
URI: MIXS:0000216
"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: samp_sort_meth\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers in\n diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nmultivalued: true\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nDuration for which the sample was stored
URI: MIXS:0000116
"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":"name: samp_store_dur\nannotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nmultivalued: false\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\n\nLocation at which sample was stored, usually name of a specific freezer/room
URI: MIXS:0000755
"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":"name: samp_store_loc\nannotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nmultivalued: false\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\n\nTemperature at which sample was stored, e.g. -80 degree Celsius
URI: MIXS:0000110
"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":"name: samp_store_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nmultivalued: false\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nName of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000999
"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":"name: samp_subtype\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nmultivalued: false\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\n\nNCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.
URI: MIXS:0001320
"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":"name: samp_taxon_id\nannotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\ndescription: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample.\n Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nmultivalued: false\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\n\nThe recent and long term history of outside sampling
URI: MIXS:0000196
"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":"name: samp_time_out\nannotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nmultivalued: false\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\n\nSample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)
URI: MIXS:0000410
"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":"name: samp_transport_cond\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nmultivalued: false\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nDepth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m
URI: MIXS:0000409
"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":"name: samp_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nmultivalued: false\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
URI: MIXS:0000998
"},{"location":"samp_type/#inheritance","title":"Inheritance","text":"name: samp_type\nannotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n package, samples include types like core, rock trimmings, drill cuttings, piping\n section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n injected water, swabs, etc. For the Food Package, samples are usually categorized\n as food, body products or tissues, or environmental material. This field accepts\n terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nmultivalued: false\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nVolume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
URI: MIXS:0000111
"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":"name: samp_vol_we_dna_ext\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n extraction. Note: total sample collected should be entered under the term Sample\n Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nmultivalued: false\nalias: samp_vol_we_dna_ext\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: QuantityValue\n\nThe weather on the sampling day
URI: MIXS:0000827
"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":"name: samp_weather\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nmultivalued: false\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\n\nName of the well (e.g. BXA1123) where sample was taken
URI: MIXS:0000296
"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":"name: samp_well_name\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nmultivalued: false\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:sample_collection_day
"},{"location":"sample_collection_day/#properties","title":"Properties","text":"name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\nURI: nmdc:sample_collection_hour
"},{"location":"sample_collection_hour/#properties","title":"Properties","text":"name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\nURI: nmdc:sample_collection_minute
"},{"location":"sample_collection_minute/#properties","title":"Properties","text":"name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\nURI: nmdc:sample_collection_month
"},{"location":"sample_collection_month/#properties","title":"Properties","text":"name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\nURI: nmdc:sample_collection_site
"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":"name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:sample_collection_year
"},{"location":"sample_collection_year/#properties","title":"Properties","text":"name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\nA unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.
URI: nmdc:sample_link
"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":"Range: String
Multivalued: True
Recommended: True
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n the field will link with the soil used in an incubation. The soil a plant was grown\n in links to the plant sample. An original culture sample was transferred to a new\n vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nmultivalued: true\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.
URI: nmdc:sample_shipped
"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":"Range: String
Recommended: True
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nType of sample being submitted
URI: nmdc:sample_type
"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":"Range: SampleTypeEnum
Recommended: True
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: sample_type_enum\nrecommended: true\n\nURI: nmdc:sampling_method
"},{"location":"sampling_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MaterialSamplingActivity no"},{"location":"sampling_method/#properties","title":"Properties","text":"name: sampling_method\ntitle: sampling method\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampling_method\ndomain_of:\n- MaterialSamplingActivity\nrange: SamplingMethodEnum\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000131
"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":"name: saturates_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nmultivalued: false\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal size in bp of all scaffolds.
URI: nmdc:scaf_bp
"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":"name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
URI: nmdc:scaf_l50
"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":"name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
URI: nmdc:scaf_l90
"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":"name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all scaffolds of that length or longer contains\n at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal size in bp of all scaffolds greater than 50 KB.
URI: nmdc:scaf_l_gt50k
"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase
URI: nmdc:scaf_logsum
"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":"name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum scaffold length.
URI: nmdc:scaf_max
"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":"name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
URI: nmdc:scaf_n50
"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":"name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n defined as the smallest number of scaffolds whose length sum makes up half of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
URI: nmdc:scaf_n90
"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":"name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of scaffolds greater than 50 KB.
URI: nmdc:scaf_n_gt50k
"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence size percentage of scaffolds greater than 50 KB.
URI: nmdc:scaf_pct_gt50k
"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:scaf_powsum
"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":"name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of all scaffolds.
URI: nmdc:scaffolds
"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":"name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThis document assumes knowledge of JSON. It also assumes rudimentary familiarity with JSON-Schema but don't worry if you are not an expert on this.
We can conceive of validation of a piece of JSON at two levels
It is crucial that the JSON is syntactically valid, otherwise it can't even be schema-validated.
There are a variety of ways to check for this. We recommend using jsonschema to validate this, see below.
NOTE: all NMDC JSON-producing tools, libraries, or scripts SHOULD use a standard json library. If you are using a robust standard json library, your output is practically guaranteed to be syntactically valid JSON.
It is strongly recommended that you do NOT generate JSON by methods such as directly manipulating json strings or printing directly. This is guaranteed to be fragile/non-robust. Even if your code works now, it is certain it will fail later and produce incorrect JSON.
For Python, there is only one choice:
https://docs.python.org/3/library/json.html
If you are not using this, you should
"},{"location":"schema-validation/#schema-validation","title":"Schema validation","text":"The JSON-Schema for NMDC is maintained in this github repo, under jsonschema/nmdc.schema.json
Note that the JSON-Schema is generated from a higher level YAML representation, using a modeling framework called linkML. See the README for details. For understanding the schema, you may be better looking at the auto-generated docs. However, for computational conformance, the JSON-Schema is what should be used.
There are a variety of json schema validators, these will give the same results. There are web playgrounds for this. But for simplicity we recommend the Python jsonschema package
To install:
pip install jsonschema\nAssume you have a file MYFILE that is json intended to conform
jsonschema -i /PATH/TO/MYFILE.json jsonschema/nmdc.schema.json\nIf the json is valid, there will be no output and the script will pass. If there are problems these will be reported.
You can try this with some ready-made examples in this repo:
jsonschema -i examples/nmdc-01.json jsonschema/nmdc.schema.json\nNote: nmdc.schema.json describes each model object, its required attributes and attribute types. The examples themselves use JSON notation to allow multiple instances of the objects in the JSON schema, to be submitted in one file.
You can also use the jsonschema library to validate directly from within your python.
"},{"location":"schema-validation/#what-to-do-if-your-json-does-not-validate","title":"What to do if your JSON does not validate","text":"There are 3 possibilities:
For 1, you can go right ahead and make PR on the schema yaml. However, if you are not comfortable doing this then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue.
For 2, this is upon you to fix this, however debugging can be aided in pulling out single instances of your model objects, and verifying that you are creating valid JSON (ie: paste one instance of your object into https://jsonlint.com/ or tools like it to verify its syntax). Another common issue is that you might have incorrect syntax for grouping many instances of a JSON object into an array. Using a small subsample of your data and an online linter as above, can aide in debugging this. Sometimes the validation can complain about invalid syntax if the attribute of an instance object disagrees with the schema's typing (ie: you have an integer where a string is expected).
"},{"location":"schema-validation/#nmdc-producer-sop","title":"NMDC Producer SOP","text":"It is expected that different providers of JSON within the NMDC take responsibility for validating their JSON. Aim1 can help with any problems.
Currently not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In future we would like to move towards a situation where all information is provided as JSON.
"},{"location":"season/","title":"Slot: season","text":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
URI: MIXS:0000829
"},{"location":"season/#inheritance","title":"Inheritance","text":"name: season\nannotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms listed\n under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nmultivalued: false\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\n\nTreatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment
URI: MIXS:0001068
"},{"location":"season_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: season_environment\nannotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nmultivalued: true\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000645
"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":"name: season_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nmultivalued: false\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMean seasonal temperature
URI: MIXS:0000643
"},{"location":"season_temp/#inheritance","title":"Inheritance","text":"name: season_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nmultivalued: false\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe seasons the space is occupied
URI: MIXS:0000830
"},{"location":"season_use/#inheritance","title":"Inheritance","text":"name: season_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nmultivalued: false\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\n\nThe process for substantially degrading the biological content of the sewage
URI: MIXS:0000351
"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":"name: secondary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process for substantially degrading the biological content of the\n sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nmultivalued: false\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about the sediment type based on major constituents
URI: MIXS:0001078
"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":"name: sediment_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nmultivalued: false\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\n\nSequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
URI: MIXS:0000050
"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":"name: seq_meth\nannotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nmultivalued: false\nalias: seq_meth\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nIndicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA
URI: MIXS:0000051
"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":"name: seq_quality_check\nannotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nmultivalued: false\nalias: seq_quality_check\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nThe ID of the landmark used to establish the coordinate system for the current feature.
URI: nmdc:seqid
"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":"name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\nURI: nmdc:sequencing_field
"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":"name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\nType of wastewater treatment plant as municipial or industrial
URI: MIXS:0000215
"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":"name: sewage_type\nannotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nmultivalued: false\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nSigns of the presence of mold or mildew on the shading device
URI: MIXS:0000834
"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":"name: shad_dev_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nmultivalued: false\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\n\nThe physical condition of the shading device at the time of sampling
URI: MIXS:0000831
"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":"name: shading_device_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nmultivalued: false\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\n\nThe location of the shading device in relation to the built structure
URI: MIXS:0000832
"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":"name: shading_device_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nmultivalued: false\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe material the shading device is composed of
URI: MIXS:0000245
"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":"name: shading_device_mat\nannotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nmultivalued: false\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of shading device
URI: MIXS:0000835
"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":"name: shading_device_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nmultivalued: false\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\n\nCollection design of pooled samples and/or sieve size and amount of sample sieved
URI: MIXS:0000322
"},{"location":"sieving/#inheritance","title":"Inheritance","text":"name: sieving\nannotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nmultivalued: false\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of silicate
URI: MIXS:0000184
"},{"location":"silicate/#inheritance","title":"Inheritance","text":"name: silicate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nmultivalued: false\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nFiltering pore size used in sample preparation
URI: MIXS:0000017
"},{"location":"size_frac/#inheritance","title":"Inheritance","text":"name: size_frac\nannotations:\n expected_value:\n tag: expected_value\n value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nmultivalued: false\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\n\nRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
URI: MIXS:0000735
"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":"name: size_frac_low\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nmultivalued: false\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
URI: MIXS:0000736
"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":"name: size_frac_up\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nmultivalued: false\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
URI: MIXS:0000647
"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":"name: slope_aspect\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n This measure provides an indication of sun and wind exposure that will influence\n soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nmultivalued: false\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCommonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
URI: MIXS:0000646
"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":"name: slope_gradient\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This measure\n is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nmultivalued: false\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe time activated sludge remains in reactor
URI: MIXS:0000669
"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":"name: sludge_retent_time\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nmultivalued: false\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:smarts_string
"},{"location":"smarts_string/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Reaction An individual biochemical transformation carried out by a functional unit of ... no"},{"location":"smarts_string/#properties","title":"Properties","text":"name: smarts_string\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smarts_string\ndomain_of:\n- Reaction\nrange: string\n\nA string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
URI: nmdc:smiles
"},{"location":"smiles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"smiles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: smiles\ndomain_of:\n- ChemicalEntity\nrange: string\n\nSodium concentration in the sample
URI: MIXS:0000428
"},{"location":"sodium/#inheritance","title":"Inheritance","text":"name: sodium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nmultivalued: false\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:soil_annual_season_temp
"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":"name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\nSpecific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath
URI: MIXS:0001082
"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":"name: soil_horizon\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nmultivalued: false\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\n\nThe relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
URI: MIXS:0000335
"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":"name: soil_text_measure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nmultivalued: false\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining soil texture
URI: MIXS:0000336
"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":"name: soil_texture_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nmultivalued: false\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\n\nDescription of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.
URI: MIXS:0000332
"},{"location":"soil_type/#inheritance","title":"Inheritance","text":"name: soil_type\nannotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be\n separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nmultivalued: false\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\n\nReference or method used in determining soil series name or other lower-level classification
URI: MIXS:0000334
"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":"name: soil_type_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nmultivalued: false\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe amount of solar energy that arrives at a specific area of a surface during a specific time interval
URI: MIXS:0000112
"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":"name: solar_irradiance\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nmultivalued: false\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
URI: MIXS:0000672
"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_inorg_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nmultivalued: true\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:soluble_iron_micromol
"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":"name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.
URI: MIXS:0000673
"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_org_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nmultivalued: true\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of soluble reactive phosphorus
URI: MIXS:0000738
"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":"name: soluble_react_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nmultivalued: false\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
URI: MIXS:0000026
"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":"name: source_mat_id\nannotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n and as opposed to a particular digital record of a material sample) used for extracting\n nucleic acids, and subsequent sequencing. The identifier can refer either to the\n original material collected or to any derived sub-samples. The INSDC qualifiers\n /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n voucher and sampled tissue with the same identifier. However, the /culture_collection\n qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n would refer to an identifier from some derived culture from which the nucleic acids\n were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nmultivalued: false\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\n\nCustomary or normal state of the space
URI: MIXS:0000770
"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":"name: space_typ_state\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nmultivalued: false\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
URI: MIXS:0000836
"},{"location":"specific/#inheritance","title":"Inheritance","text":"name: specific\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nmultivalued: false\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\n\nSpecific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.
URI: nmdc:specific_ecosystem
"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":"name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nThe mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.
URI: MIXS:0000214
"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":"name: specific_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nmultivalued: false\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSource rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000996
"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":"name: sr_dep_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nmultivalued: false\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\n\nGeological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period(geology)). If \"other\" is specified, please propose entry in \"additional info\" field_
URI: MIXS:0000997
"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":"name: sr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nmultivalued: false\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\n\nOrigin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000994
"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":"name: sr_kerog_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nmultivalued: false\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\n\nLithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000995
"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":"name: sr_lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nmultivalued: false\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\n\nTreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0001069
"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: standing_water_regm\nannotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n span, types can be flood water or standing water, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nmultivalued: true\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe start of the feature in positive 1-based integer coordinates
URI: nmdc:start
"},{"location":"start/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was started
URI: nmdc:start_date
"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PlannedProcess no Pooling physical combination of several instances of like material no Extraction A material separation in which a desired component of an input material is se... no LibraryPreparation no CollectingBiosamplesFromSite no BiosampleProcessing A process that takes one or more biosamples as inputs and generates one or mo... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no"},{"location":"start_date/#properties","title":"Properties","text":"name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nDate the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_date_inc
"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: 2021-04-15, 2021-04 and 2021 are all acceptable.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_time_inc
"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: 13:33 or 13:33:55\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:started_at_time
"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"started_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- Activity\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nURI: nmdc:status
"},{"location":"status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QualityControlReport no"},{"location":"status/#properties","title":"Properties","text":"name: status\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: status\ndomain_of:\n- QualityControlReport\nrange: StatusEnum\n\nfrom reaction participant class
URI: nmdc:stoichiometry
"},{"location":"stoichiometry/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReactionParticipant Instances of this link a reaction to a chemical entity participant no"},{"location":"stoichiometry/#properties","title":"Properties","text":"name: stoichiometry\ndescription: from reaction participant class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stoichiometry\ndomain_of:\n- ReactionParticipant\nrange: integer\n\nExplain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).
URI: MIXS:0000327
"},{"location":"store_cond/#inheritance","title":"Inheritance","text":"name: store_cond\nannotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nmultivalued: false\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).
URI: nmdc:strand
"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":"name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n or forward strand) or '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\nThe type of research initiative
URI: nmdc:study_category
"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":"name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\n\nURI: nmdc:study_identifiers
"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nmultivalued: true\nalias: study_identifiers\nrange: external_identifier\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nLinks a study to one or more images.
URI: nmdc:study_image
"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":"Range: ImageValue
Multivalued: True
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: Study\nmultivalued: true\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\ninlined: true\n\nThis property links a database object to the set of studies within it.
URI: nmdc:study_set
"},{"location":"study_set/#inheritance","title":"Inheritance","text":"Range: Study
Multivalued: True
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\ndomain: Database\nmultivalued: true\nalias: study_set\ndomain_of:\n- Database\nrange: Study\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:subject
"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no"},{"location":"subject/#properties","title":"Properties","text":"name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\nrange: GeneProduct\n\nThe substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
URI: MIXS:0000767
"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":"Range: SubstructureTypeEnum
Multivalued: True
name: substructure_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The substructure or under building is that largely hidden section of\n the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nmultivalued: true\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\n\nURI: nmdc:subsurface_depth
"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":"name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfate in the sample
URI: MIXS:0000423
"},{"location":"sulfate/#inheritance","title":"Inheritance","text":"name: sulfate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nmultivalued: false\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal sulfate concentration in the hydrocarbon resource
URI: MIXS:0000407
"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":"name: sulfate_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nmultivalued: false\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfide in the sample
URI: MIXS:0000424
"},{"location":"sulfide/#inheritance","title":"Inheritance","text":"name: sulfide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nmultivalued: false\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nContaminant identified on surface
URI: MIXS:0000759
"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":"Range: SurfAirContEnum
Multivalued: True
name: surf_air_cont\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nmultivalued: true\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\n\nSurfaces: water activity as a function of air and material moisture
URI: MIXS:0000123
"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":"name: surf_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nmultivalued: false\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSurface materials at the point of sampling
URI: MIXS:0000758
"},{"location":"surf_material/#inheritance","title":"Inheritance","text":"name: surf_material\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nmultivalued: false\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\n\nWater held on a surface
URI: MIXS:0000128
"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":"name: surf_moisture\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nmultivalued: false\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nph measurement of surface
URI: MIXS:0000760
"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":"name: surf_moisture_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nmultivalued: false\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\n\nTemperature of the surface at the time of sampling
URI: MIXS:0000125
"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":"name: surf_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nmultivalued: false\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of suspended particulate matter
URI: MIXS:0000741
"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":"name: suspend_part_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nmultivalued: false\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
URI: MIXS:0000150
"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: suspend_solids\nannotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances including a wide variety of material, such\n as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nmultivalued: true\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\n\nTotal Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)
URI: MIXS:0000120
"},{"location":"tan/#inheritance","title":"Inheritance","text":"name: tan\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nmultivalued: false\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTargeted gene or locus name for marker gene studies
URI: MIXS:0000044
"},{"location":"target_gene/#inheritance","title":"Inheritance","text":"name: target_gene\nannotations:\n expected_value:\n tag: expected_value\n value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nmultivalued: false\nalias: target_gene\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nName of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
URI: MIXS:0000045
"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":"name: target_subfragment\nannotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nmultivalued: false\nalias: target_subfragment\ndomain_of:\n- Biosample\n- OmicsProcessing\nrange: TextValue\n\nIf sending technical replicates of the same sample, indicate the replicate count.
URI: nmdc:technical_reps
"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":"Range: String
Recommended: True
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nTemperature of the sample at the time of sampling.
URI: MIXS:0000113
"},{"location":"temp/#inheritance","title":"Inheritance","text":"name: temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nmultivalued: false\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe recorded temperature value at sampling time outside
URI: MIXS:0000197
"},{"location":"temp_out/#inheritance","title":"Inheritance","text":"name: temp_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nmultivalued: false\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\n\npointer to an ontology class
URI: nmdc:term
"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes"},{"location":"term/#properties","title":"Properties","text":"name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\ndomain: ControlledTermValue\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\nThe process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
URI: MIXS:0000352
"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":"name: tertiary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nmultivalued: false\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\n\nStage of tide
URI: MIXS:0000750
"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":"name: tidal_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nmultivalued: false\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\n\nNote method(s) used for tilling
URI: MIXS:0001081
"},{"location":"tillage/#inheritance","title":"Inheritance","text":"Range: TillageEnum
Multivalued: True
name: tillage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nmultivalued: true\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\n\nDescription of plant tissue culture growth media used
URI: MIXS:0001070
"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":"name: tiss_cult_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nmultivalued: false\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\n\nA name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.
URI: nmdc:title
"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":"name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the GOLD\n system has assigned a name/label. However, for display purposes, we may also wish\n the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\nConcentration of toluene in the sample
URI: MIXS:0000154
"},{"location":"toluene/#inheritance","title":"Inheritance","text":"name: toluene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nmultivalued: false\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:too_short_contig_num
"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":"name: too_short_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nTotal carbon content
URI: MIXS:0000525
"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":"name: tot_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nmultivalued: false\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of total depth of water column
URI: MIXS:0000634
"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":"name: tot_depth_water_col\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nmultivalued: false\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
URI: MIXS:0000744
"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":"name: tot_diss_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nmultivalued: false\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal inorganic nitrogen content
URI: MIXS:0000745
"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":"name: tot_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nmultivalued: false\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of total iron in the sample
URI: MIXS:0000105
"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":"name: tot_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nmultivalued: false\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
URI: MIXS:0000102
"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":"name: tot_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nmultivalued: false\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining the total nitrogen
URI: MIXS:0000338
"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":"name: tot_nitro_cont_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nmultivalued: false\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\n\nTotal nitrogen content of the sample
URI: MIXS:0000530
"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":"name: tot_nitro_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nmultivalued: false\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nReference or method used in determining total organic carbon
URI: MIXS:0000337
"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":"name: tot_org_c_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nmultivalued: false\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\n\nDefinition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
URI: MIXS:0000533
"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":"name: tot_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nmultivalued: false\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal particulate carbon content
URI: MIXS:0000747
"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":"name: tot_part_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nmultivalued: false\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
URI: MIXS:0000117
"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":"name: tot_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nmultivalued: false\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTotal amount or concentration of phosphate
URI: MIXS:0000689
"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":"name: tot_phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nmultivalued: false\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of total sulfur in the sample
URI: MIXS:0000419
"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":"name: tot_sulfur\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nmultivalued: false\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:total_bases
"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":"name: total_bases\ntodos:\n- this slot needs some basic textual annotations and constraints\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: string\n\nThe subway line name
URI: MIXS:0000837
"},{"location":"train_line/#inheritance","title":"Inheritance","text":"name: train_line\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nmultivalued: false\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\n\nThe train station collection location
URI: MIXS:0000838
"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":"name: train_stat_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nmultivalued: false\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\n\nThe train stop collection location
URI: MIXS:0000839
"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":"name: train_stop_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nmultivalued: false\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\n\nMeasure of the amount of cloudiness or haziness in water caused by individual particles
URI: MIXS:0000191
"},{"location":"turbidity/#inheritance","title":"Inheritance","text":"name: turbidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nmultivalued: false\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).
URI: MIXS:0000397
"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nmultivalued: false\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).
URI: MIXS:0000394
"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nmultivalued: false\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCustomary or normal density of occupants
URI: MIXS:0000771
"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":"name: typ_occup_density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nmultivalued: false\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\n\nAn optional string that specifies the type object. This is used to allow for searches for different kinds of objects.
URI: nmdc:type
"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no Biosample Biological source material which can be characterized by an experiment no Study A study summarizes the overall goal of a research initiative and outlines the... no OmicsProcessing The methods and processes used to generate omics data from a biosample or org... no CreditAssociation This class supports binding associated researchers to studies no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MagBin no GenomeFeature A feature localized to an interval along a genome yes MetatranscriptomeAssembly no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"type/#properties","title":"Properties","text":"name: type\ndescription: An optional string that specifies the type object. This is used to allow\n for searches for different kinds of objects.\ndeprecated: Due to confusion about what values are used for this slot, it is best\n not to use this slot. See https://github.com/microbiomedata/nmdc-schema/issues/248.\n MAM removed designates_type and rdf:type slot uri 2022-11-30\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: type\ndomain_of:\n- DataObject\n- Biosample\n- Study\n- OmicsProcessing\n- CreditAssociation\n- WorkflowExecutionActivity\n- MetagenomeAssembly\n- MetagenomeAnnotationActivity\n- MetatranscriptomeAnnotationActivity\n- MetatranscriptomeActivity\n- MagsAnalysisActivity\n- ReadQcAnalysisActivity\n- ReadBasedTaxonomyAnalysisActivity\n- MagBin\n- GenomeFeature\nrange: string\n\nLast generated 2023-01-12
If a class doesn't use the id slot, then there is no need to assign that class a typecode
Typecodes can be directly asserted for a class, or a class can inherit a typecode from one of its ancestors. This table does not yet indicate when a typecode was inherited from an ancestor. An example of inheritance is 'acty' for WorkflowExecutionActivity, which is inherited from it's ancestor Activity
Todo:
URI: nmdc:unbinned_contig_num
"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":"name: unbinned_contig_num\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysisActivity\nrange: integer\n\nURI: nmdc:url
"},{"location":"url/#inheritance","title":"Inheritance","text":"name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: attribute\nalias: url\ndomain_of:\n- Protocol\n- DataObject\n- ImageValue\nrange: string\n\nURI: nmdc:used
"},{"location":"used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity yes NomAnalysisActivity yes"},{"location":"used/#properties","title":"Properties","text":"name: used\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:used\nrank: 1000\ndomain: Activity\nalias: used\ndomain_of:\n- Activity\nrange: string\n\nVentilation rate of the system in the sampled premises
URI: MIXS:0000114
"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":"name: ventilation_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nmultivalued: false\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nVentilation system used in the sampled premises
URI: MIXS:0000756
"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":"name: ventilation_type\nannotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nmultivalued: false\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:version
"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"version/#properties","title":"Properties","text":"name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecutionActivity\n- ReadQcAnalysisActivity\nrange: string\n\nConcentration of Volatile Fatty Acids in the sample
URI: MIXS:0000152
"},{"location":"vfa/#inheritance","title":"Inheritance","text":"name: vfa\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nmultivalued: false\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nOriginal volatile fatty acid concentration in the hydrocarbon resource
URI: MIXS:0000408
"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":"name: vfa_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nmultivalued: false\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building visual media
URI: MIXS:0000840
"},{"location":"vis_media/#inheritance","title":"Inheritance","text":"name: vis_media\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nmultivalued: false\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\n\nA measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)
URI: MIXS:0000126
"},{"location":"viscosity/#inheritance","title":"Inheritance","text":"name: viscosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nmultivalued: false\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
URI: MIXS:0000115
"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: volatile_org_comp\nannotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n temperature; can report multiple volatile organic compounds by entering numeric\n values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nmultivalued: true\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe total area of the sampled room's walls
URI: MIXS:0000198
"},{"location":"wall_area/#inheritance","title":"Inheritance","text":"name: wall_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nmultivalued: false\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe building class of the wall defined by the composition of the building elements and fire-resistance rating.
URI: MIXS:0000841
"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":"name: wall_const_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building class of the wall defined by the composition of the building\n elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nmultivalued: false\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\n\nThe material utilized to finish the outer most layer of the wall
URI: MIXS:0000842
"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":"name: wall_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nmultivalued: false\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\n\nThe average height of the walls in the sampled room
URI: MIXS:0000221
"},{"location":"wall_height/#inheritance","title":"Inheritance","text":"name: wall_height\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nmultivalued: false\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe relative location of the wall within the room
URI: MIXS:0000843
"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":"name: wall_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nmultivalued: false\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\n\nThe surface treatment of interior wall
URI: MIXS:0000845
"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":"name: wall_surf_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nmultivalued: false\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\n\nThe feel, appearance, or consistency of a wall surface
URI: MIXS:0000846
"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":"name: wall_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nmultivalued: false\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\n\nThe ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
URI: MIXS:0000222
"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":"name: wall_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nmultivalued: false\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nSigns of the presence of mold or mildew on a wall
URI: MIXS:0000844
"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":"name: wall_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nmultivalued: false\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nURI: nmdc:was_generated_by
"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no AttributeValue The value for any value of a attribute for a sample no FunctionalAnnotation An assignment of a function term (e yes InstrumentValue no QuantityValue A simple quantity, e no ImageValue An attribute value representing an image no PersonValue An attribute value representing a person no TextValue A basic string value no UrlValue A value that is a string that conforms to URL syntax no TimestampValue A value that is a timestamp no IntegerValue A value that is an integer no BooleanValue A value that is a boolean no ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no GeolocationValue A normalized value for a location on the earth's surface no"},{"location":"was_generated_by/#properties","title":"Properties","text":"name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- DataObject\n- AttributeValue\n- FunctionalAnnotation\nrange: Activity\n\nURI: nmdc:was_informed_by
"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Activity a provence-generating activity no WorkflowExecutionActivity Represents an instance of an execution of a particular workflow no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetatranscriptomeAssembly no MetagenomeAnnotationActivity A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAnnotationActivity no MetatranscriptomeActivity A metatranscriptome activity that e no MagsAnalysisActivity A workflow execution activity that uses computational binning tools to group ... no MetagenomeSequencingActivity Initial sequencing activity that precedes any analysis no ReadQcAnalysisActivity A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysisActivity A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysisActivity no MetaproteomicsAnalysisActivity no NomAnalysisActivity no"},{"location":"was_informed_by/#properties","title":"Properties","text":"name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- Activity\nrange: Activity\n\nThe origin of wastewater such as human waste, rainfall, storm drains, etc.
URI: MIXS:0000353
"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":"name: wastewater_type\nannotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nmultivalued: false\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\n\nReference or method used in determining the water content of soil
URI: MIXS:0000323
"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":"name: water_cont_soil_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nmultivalued: false\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\n\nWater content measurement
URI: MIXS:0000185
"},{"location":"water_content/#inheritance","title":"Inheritance","text":"name: water_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nmultivalued: false\nalias: water_content\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nMeasurement of magnitude and direction of flow within a fluid
URI: MIXS:0000203
"},{"location":"water_current/#inheritance","title":"Inheritance","text":"name: water_current\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nmultivalued: false\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nCurrent amount of water (%) in a produced fluid stream; or the average of the combined streams
URI: MIXS:0000454
"},{"location":"water_cut/#inheritance","title":"Inheritance","text":"name: water_cut\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nmultivalued: false\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe size of the water feature
URI: MIXS:0000223
"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":"name: water_feat_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nmultivalued: false\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of water feature present within the building being sampled
URI: MIXS:0000847
"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":"name: water_feat_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nmultivalued: false\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\n\nWater production rates per well (e.g. 987 m3 / day)
URI: MIXS:0000453
"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":"name: water_prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nmultivalued: false\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nInformation about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000590
"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: water_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nmultivalued: true\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nInformation about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000591
"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: watering_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can include\n multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nmultivalued: true\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\n\nA list of websites that are associated with the entity.
URI: nmdc:websites
"},{"location":"websites/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes PersonValue An attribute value representing a person no"},{"location":"websites/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: websites\ndescription: A list of websites that are associated with the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmultivalued: true\nalias: websites\ndomain_of:\n- Study\n- PersonValue\nrange: string\n\nThe day of the week when sampling occurred
URI: MIXS:0000848
"},{"location":"weekday/#inheritance","title":"Inheritance","text":"name: weekday\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nmultivalued: false\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\n\nA unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)
URI: MIXS:0000297
"},{"location":"win/#inheritance","title":"Inheritance","text":"name: win\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nmultivalued: false\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\n\nWind direction is the direction from which a wind originates
URI: MIXS:0000757
"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":"name: wind_direction\nannotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nmultivalued: false\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\n\nSpeed of wind measured at the time of sampling
URI: MIXS:0000118
"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":"name: wind_speed\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nmultivalued: false\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe physical condition of the window at the time of sampling
URI: MIXS:0000849
"},{"location":"window_cond/#inheritance","title":"Inheritance","text":"name: window_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nmultivalued: false\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\n\nThe type of window covering
URI: MIXS:0000850
"},{"location":"window_cover/#inheritance","title":"Inheritance","text":"name: window_cover\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nmultivalued: false\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\n\nThe horizontal position of the window on the wall
URI: MIXS:0000851
"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":"name: window_horiz_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nmultivalued: false\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\n\nThe relative location of the window within the room
URI: MIXS:0000852
"},{"location":"window_loc/#inheritance","title":"Inheritance","text":"name: window_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nmultivalued: false\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\n\nThe type of material used to finish a window
URI: MIXS:0000853
"},{"location":"window_mat/#inheritance","title":"Inheritance","text":"name: window_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nmultivalued: false\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\n\nThe number of times windows are opened per week
URI: MIXS:0000246
"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":"name: window_open_freq\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nmultivalued: false\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe window's length and width
URI: MIXS:0000224
"},{"location":"window_size/#inheritance","title":"Inheritance","text":"name: window_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nmultivalued: false\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\n\nDefines whether the windows were open or closed during environmental testing
URI: MIXS:0000855
"},{"location":"window_status/#inheritance","title":"Inheritance","text":"name: window_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nmultivalued: false\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\n\nThe type of windows
URI: MIXS:0000856
"},{"location":"window_type/#inheritance","title":"Inheritance","text":"name: window_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nmultivalued: false\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\n\nThe vertical position of the window on the wall
URI: MIXS:0000857
"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":"name: window_vert_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nmultivalued: false\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\n\nSigns of the presence of mold or mildew on the window.
URI: MIXS:0000854
"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":"name: window_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nmultivalued: false\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\n\nConcentration of xylene in the sample
URI: MIXS:0000156
"},{"location":"xylene/#inheritance","title":"Inheritance","text":"name: xylene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nmultivalued: false\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of zinc in the sample
URI: nmdc:zinc
"},{"location":"zinc/#inheritance","title":"Inheritance","text":"name: zinc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nis_a: attribute\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n