diff --git a/schema_sheets/populated_tsv/slot_usage_minimal.tsv b/schema_sheets/populated_tsv/slot_usage_minimal.tsv index 4243de36..3d39f60f 100644 --- a/schema_sheets/populated_tsv/slot_usage_minimal.tsv +++ b/schema_sheets/populated_tsv/slot_usage_minimal.tsv @@ -27,128 +27,68 @@ sediment_data aggregation slot relating sediment data collections to a Sa soil_data aggregation slot relating soil data collections to a SampleData container true SoilInterface wastewater_sludge_data aggregation slot relating wastewater_sludge data collections to a SampleData container true WastewaterSludgeInterface water_data aggregation slot relating water data collections to a SampleData container true WaterInterface -project_id Proposal IDs or names associated with dataset true {text} project ID -sample_type This can vary from 'environmental package' if the sample is an extraction. Type of sample being submitted water extracted soil sample_type_enum true sample type -sample_shipped This field is only required when completing metadata for samples being submitted to EMSL for analyses. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. 15 g|100 uL|5 mL true {float} {unit} sample shipped amount -emsl_store_temp Enter a temperature in celsius. Numeric portion only. The temperature at which the sample should be stored upon delivery to EMSL -80 true {float} EMSL sample storage temperature, deg. C add 'see_alsos' with link to NEXUS info -technical_reps This field is only required when completing metadata for samples being submitted to EMSL for analyses. If sending technical replicates of the same sample, indicate the replicate count. 2 true {integer} number technical replicate -replicate_number This will guide staff in ensuring your samples are block & randomized correctly If sending biological replicates, indicate the rep number here. true {integer} replicate number -dna_seq_project Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 true {text} DNA seq project ID -dna_seq_project_name Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metagenomics true {text} DNA seq project name -dna_samp_id Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 true {text} DNA sample ID Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled? -dna_sample_name Give 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. JGI_pond_041618 true {text} DNA sample name -dna_concentration Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 2000 0 float true {float} DNA concentration in ng/ul -dna_volume Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 1000 0 float true {float} DNA volume in ul -dna_absorb1 Recommended value is between 1 and 3. 260/280 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/280 -dna_absorb2 Recommended value is between 1 and 3. 260/230 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/230 -dna_container_id Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 true {text < 20 characters} DNA container label -dna_cont_type Tube or plate (96-well) plate dna_cont_type_enum true DNA container type -dna_cont_well Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ true {96 well plate pos} DNA plate position -dna_sample_format Solution in which the DNA sample has been suspended Water dna_sample_format_enum true DNA sample format -dna_dnase Note DNase treatment is required for all RNA samples. no YesNoEnum true DNase treatment DNA -dna_organisms List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) true {text} DNA expected organisms -dna_collect_site Provide information on the site your DNA sample was collected from untreated pond water true {text} DNA collection site -dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction true {text} DNA isolation method -dna_seq_project_pi Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson true {text} DNA seq project PI -dna_project_contact Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones true {text} DNA seq project contact -proposal_dna Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 true {text} DNA proposal ID -rna_seq_project Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 true {text} RNA seq project ID -rna_seq_project_name Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metatranscriptomics true {text} RNA seq project name -rna_samp_id Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 true {text} RNA sample ID -rna_sample_name Give 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. JGI_pond_041618 2000 0 true {text} RNA sample name -rna_concentration Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 1000 0 float true {float} RNA concentration in ng/ul -rna_volume Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 float true {float} RNA volume in ul -rna_absorb1 Recommended value is between 1 and 3. 260/280 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/280 -rna_absorb2 Recommended value is between 1 and 3. 260/230 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/230 -rna_container_id Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 true {text} RNA container label -rna_cont_type Tube or plate (96-well) plate rna_cont_type_enum true RNA container type -rna_cont_well Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ true {96 well plate pos} RNA plate position -rna_sample_format Solution in which the RNA sample has been suspended Water rna_sample_format_enum true RNA sample format -dnase_rna Note DNase treatment is required for all RNA samples. no YesNoEnum true DNase treated -rna_organisms List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) true {text} RNA expected organisms -rna_collect_site Provide information on the site your RNA sample was collected from untreated pond water true {text} RNA collection site -rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction true {text} RNA isolation method -rna_seq_project_pi Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson true {text} RNA seq project PI -rna_project_contact Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones true {text} RNA seq project contact -proposal_rna Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 true {text} RNA proposal ID -alkalinity alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false string MIXS:0000421 alkalinity -alkyl_diethers alkyl diethers measurement value mole per liter 1 Concentration of alkyl diethers 0.005 mole per liter false string MIXS:0000490 alkyl diethers -aminopept_act aminopeptidase activity measurement value mole per liter per hour 1 Measurement of aminopeptidase activity 0.269 mole per liter per hour false string MIXS:0000172 aminopeptidase activity -ammonium ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false string MIXS:0000427 ammonium -bacteria_carb_prod bacterial carbon production measurement value nanogram per hour 1 Measurement of bacterial carbon production 2.53 microgram per liter per hour false string MIXS:0000173 bacterial carbon production -biomass biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false string MIXS:0000174 {text};{float} {unit} biomass -bishomohopanol bishomohopanol measurement value microgram per liter, microgram per gram 1 Concentration of bishomohopanol 14 microgram per liter false string MIXS:0000175 bishomohopanol -bromide bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false string MIXS:0000176 bromide -calcium calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false string MIXS:0000432 calcium -chloride chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false string MIXS:0000429 chloride -chlorophyll chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false string MIXS:0000177 chlorophyll -density density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false string MIXS:0000435 density -diether_lipids diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false string MIXS:0000178 {text};{float} {unit} diether lipids -diss_carb_dioxide dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false string MIXS:0000436 dissolved carbon dioxide -diss_hydrogen dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false string MIXS:0000179 dissolved hydrogen -diss_inorg_carb dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false string MIXS:0000434 dissolved inorganic carbon -diss_org_carb dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false string MIXS:0000433 dissolved organic carbon -diss_org_nitro dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false string MIXS:0000162 dissolved organic nitrogen -diss_oxygen dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false string MIXS:0000119 dissolved oxygen -glucosidase_act glucosidase activity measurement value mol per liter per hour 1 Measurement of glucosidase activity 5 mol per liter per hour false string MIXS:0000137 glucosidase activity -magnesium magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false string MIXS:0000431 magnesium -mean_frict_vel mean friction velocity measurement value meter per second 1 Measurement of mean friction velocity 0.5 meter per second false string MIXS:0000498 mean friction velocity -mean_peak_frict_vel mean peak friction velocity measurement value meter per second 1 Measurement of mean peak friction velocity 1 meter per second false string MIXS:0000502 mean peak friction velocity -methane methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false string MIXS:0000101 methane -n_alkanes n-alkanes n-alkane name;measurement value micromole per liter m Concentration of n-alkanes; can include multiple n-alkanes n-hexadecane;100 milligram per liter false string MIXS:0000503 {text};{float} {unit} n-alkanes -nitrate nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false string MIXS:0000425 nitrate -nitrite nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false string MIXS:0000426 nitrite -nitro nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false string MIXS:0000504 nitrogen -org_carb organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false string MIXS:0000508 organic carbon -organism_count organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false string MIXS:0000103 organism count -part_org_carb particulate organic carbon measurement value microgram per liter 1 Concentration of particulate organic carbon 1.92 micromole per liter false string MIXS:0000515 particulate organic carbon -particle_class particle classification particle name;measurement value micrometer m Particles 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 false string MIXS:0000206 {text};{float} {unit} particle classification -perturbation perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation -petroleum_hydrocarb petroleum hydrocarbon measurement value micromole per liter 1 Concentration of petroleum hydrocarbon 0.05 micromole per liter false string MIXS:0000516 petroleum hydrocarbon -phaeopigments phaeopigments phaeopigment name;measurement value milligram per cubic meter m Concentration of phaeopigments; can include multiple phaeopigments 2.5 milligram per cubic meter false string MIXS:0000180 {text};{float} {unit} phaeopigments -phosplipid_fatt_acid phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid -porosity porosity measurement value or range percentage 1 Porosity of deposited sediment is volume of voids divided by the total volume of sample false string MIXS:0000211 {float} - {float} {unit} porosity -potassium potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false string MIXS:0000430 potassium -pressure pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false string MIXS:0000412 pressure -redox_potential redox potential measurement value millivolt 1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential 300 millivolt false string MIXS:0000182 redox potential -samp_store_loc sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location -sediment_type sediment type enumeration 1 Information about the sediment type based on major constituents biogenous false sediment_type_enum MIXS:0001078 sediment type -silicate silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false string MIXS:0000184 silicate -sulfate sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false string MIXS:0000423 sulfate -tidal_stage tidal stage enumeration 1 Stage of tide high tide false tidal_stage_enum MIXS:0000750 tidal stage -tot_depth_water_col total depth of water column measurement value meter 1 Measurement of total depth of water column 500 meter false string MIXS:0000634 total depth of water column -turbidity turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false string MIXS:0000191 turbidity -air_PM_concen air particulate matter concentration particulate matter name;measurement value micrograms per cubic meter m Concentration 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 PM2.5;10 microgram per cubic meter false string MIXS:0000108 {text};{float} {unit} air particulate matter concentration -barometric_press barometric pressure measurement value millibar 1 Force per unit area exerted against a surface by the weight of air above that surface 5 millibar false string MIXS:0000096 barometric pressure -carb_dioxide carbon dioxide measurement value micromole per liter, parts per million 1 Carbon dioxide (gas) amount or concentration at the time of sampling 410 parts per million false string MIXS:0000097 carbon dioxide -carb_monoxide carbon monoxide measurement value micromole per liter, parts per million 1 Carbon monoxide (gas) amount or concentration at the time of sampling 0.1 parts per million false string MIXS:0000098 carbon monoxide -humidity humidity measurement value gram per cubic meter 1 Amount of water vapour in the air, at the time of sampling 25 gram per cubic meter false string MIXS:0000100 humidity -oxygen oxygen measurement value milligram per liter, parts per million 1 Oxygen (gas) amount or concentration at the time of sampling 600 parts per million false string MIXS:0000104 oxygen -pollutants pollutants pollutant name;measurement value gram, mole per liter, milligram per liter, microgram per cubic meter m Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant lead;0.15 microgram per cubic meter false string MIXS:0000107 {text};{float} {unit} pollutants -solar_irradiance solar irradiance measurement value kilowatts per square meter per day, ergs per square centimeter per second 1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval 1.36 kilowatts per square meter per day false string MIXS:0000112 solar irradiance -ventilation_rate ventilation rate measurement value cubic meter per minute, liters per second 1 Ventilation rate of the system in the sampled premises 750 cubic meter per minute false string MIXS:0000114 ventilation rate -ventilation_type ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type -volatile_org_comp volatile organic compounds volatile organic compound name;measurement value microgram per cubic meter, parts per million, nanogram per liter m Concentration 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 formaldehyde;500 nanogram per liter false string MIXS:0000115 {text};{float} {unit} volatile organic compounds -wind_direction wind direction wind direction name 1 Wind direction is the direction from which a wind originates Northwest false string MIXS:0000757 {text} wind direction -wind_speed wind speed measurement value meter per second, kilometer per hour 1 Speed of wind measured at the time of sampling 21 kilometer per hour false string MIXS:0000118 wind speed abs_air_humidity absolute air humidity measurement value gram per gram, kilogram per kilogram, kilogram, pound 1 Actual mass of water vapor - mh20 - present in the air water vapor mixture 9 gram per gram false string MIXS:0000122 absolute air humidity +add_recov_method secondary and tertiary recovery methods and start date enumeration;timestamp 1 "Additional (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" Polymer Addition;2018-06-21T14:30Z false string MIXS:0001009 secondary and tertiary recovery methods and start date +additional_info additional info text 1 Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary false string MIXS:0000300 {text} additional info address address value 1 The street name and building number where the sampling occurred. false string MIXS:0000218 {integer}{text} address adj_room adjacent rooms room name;room number 1 List of rooms (room number, room name) immediately adjacent to the sampling room false string MIXS:0000219 {text};{integer} adjacent rooms aero_struc aerospace structure enumeration 1 Aerospace 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 plane false string MIXS:0000773 [plane|glider] aerospace structure +agrochem_addition history/agrochemical additions agrochemical name;agrochemical amount;timestamp gram, mole per liter, milligram per liter m Addition of fertilizers, pesticides, etc. - amount and time of applications roundup;5 milligram per liter;2018-06-21 false string MIXS:0000639 {text};{float} {unit};{timestamp} history/agrochemical additions +air_PM_concen air particulate matter concentration particulate matter name;measurement value micrograms per cubic meter m Concentration 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 PM2.5;10 microgram per cubic meter false string MIXS:0000108 {text};{float} {unit} air particulate matter concentration air_temp air temperature measurement value degree Celsius 1 Temperature of the air at the time of sampling 20 degree Celsius false string MIXS:0000124 air temperature +air_temp_regm air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen +al_sat extreme_unusual_properties/Al saturation measurement value percentage 1 Aluminum saturation (esp. For tropical soils) false string MIXS:0000607 extreme_unusual_properties/Al saturation +al_sat_meth extreme_unusual_properties/Al saturation method PMID,DOI or URL 1 Reference or method used in determining Al saturation false string MIXS:0000324 {PMID}|{DOI}|{URL} extreme_unusual_properties/Al saturation method +alkalinity alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false string MIXS:0000421 alkalinity +alkalinity_method alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method +alkyl_diethers alkyl diethers measurement value mole per liter 1 Concentration of alkyl diethers 0.005 mole per liter false string MIXS:0000490 alkyl diethers +alt altitude measurement value Altitude 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 100 meter false string MIXS:0000094 altitude +aminopept_act aminopeptidase activity measurement value mole per liter per hour 1 Measurement of aminopeptidase activity 0.269 mole per liter per hour false string MIXS:0000172 aminopeptidase activity +ammonium ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false string MIXS:0000427 ammonium +ammonium_nitrogen ammonium_nitrogen|NH4-N measurement value mg/kg 1 Concentration of ammonium nitrogen in the sample 2.3 mg/kg false string ammonium nitrogen amount_light amount of light measurement value lux, lumens per square meter 1 The unit of illuminance and luminous emittance, measuring luminous flux per unit area false string MIXS:0000140 amount of light +analysis_type Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type +ances_data ancestral data free text 1 Information 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) A/3*B false string MIXS:0000247 {text} ancestral data +annual_precpt mean annual precipitation measurement value millimeter 1 The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. false string MIXS:0000644 mean annual precipitation +annual_temp mean annual temperature measurement value degree Celsius 1 Mean annual temperature 12.5 degree Celsius false string MIXS:0000642 mean annual temperature +antibiotic_regm antibiotic regimen antibiotic name;antibiotic amount;treatment interval and duration milligram m Information 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 penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000553 {text};{float} {unit};{Rn/start_time/end_time/duration} antibiotic regimen +api API gravity measurement value degrees API 1 API 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¬∞ API) false string MIXS:0000157 API gravity arch_struc architectural structure enumeration 1 An architectural structure is a human-made, free-standing, immobile outdoor construction shed false arch_struc_enum MIXS:0000774 architectural structure +aromatics_pc aromatics wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000133 {text};{float} {unit} aromatics wt% +asphaltenes_pc asphaltenes wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000135 {text};{float} {unit} asphaltenes wt% +atmospheric_data atmospheric data atmospheric data name;measurement value m Measurement of atmospheric data; can include multiple data wind speed;9 knots false string MIXS:0001097 {text};{float} {unit} atmospheric data avg_dew_point average dew point measurement value degree Celsius 1 The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day 25.5 degree Celsius false string MIXS:0000141 average dew point avg_occup average daily occupancy value 1 Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. 2 false string MIXS:0000775 average daily occupancy avg_temp average temperature measurement value degree Celsius 1 The average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day 12.5 degree Celsius false string MIXS:0000142 average temperature +bac_prod bacterial production measurement value milligram per cubic meter per day 1 Bacterial production in the water column measured by isotope uptake 5 milligram per cubic meter per day false string MIXS:0000683 bacterial production +bac_resp bacterial respiration measurement value milligram per cubic meter per day, micromole oxygen per liter per hour 1 Measurement of bacterial respiration in the water column 300 micromole oxygen per liter per hour false string MIXS:0000684 bacterial respiration +bacteria_carb_prod bacterial carbon production measurement value nanogram per hour 1 Measurement of bacterial carbon production 2.53 microgram per liter per hour false string MIXS:0000173 bacterial carbon production +barometric_press barometric pressure measurement value millibar 1 Force per unit area exerted against a surface by the weight of air above that surface 5 millibar false string MIXS:0000096 barometric pressure +basin basin name name 1 Name of the basin (e.g. Campos) false string MIXS:0000290 {text} basin name bathroom_count bathroom count value 1 The number of bathrooms in the building 1 false string MIXS:0000776 bathroom count bedroom_count bedroom count value 1 The number of bedrooms in the building 2 false string MIXS:0000777 bedroom count +benzene benzene measurement value milligram per liter, parts per million 1 Concentration of benzene in the sample false string MIXS:0000153 benzene +biochem_oxygen_dem biochemical oxygen demand measurement value milligram per liter 1 Amount 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 false string MIXS:0000653 biochemical oxygen demand +biocide biocide administration name;name;timestamp 1 List of biocides (commercial name of product and supplier) and date of administration ALPHA 1427;Baker Hughes;2008-01-23 false string MIXS:0001011 {text};{text};{timestamp} biocide administration +biocide_admin_method biocide administration method measurement value;frequency;duration;duration milligram per liter 1 Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) false string MIXS:0000456 {float} {unit};{Rn/start_time/end_time/duration};{duration} biocide administration method +biol_stat biological status enumeration 1 The level of genome modification. natural false biol_stat_enum MIXS:0000858 biological status +biomass biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false string MIXS:0000174 {text};{float} {unit} biomass +biotic_regm biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string MIXS:0001038 {text} biotic regimen +biotic_relationship observed biotic relationship enumeration Description 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 free living false biotic_relationship_enum MIXS:0000028 observed biotic relationship +bishomohopanol bishomohopanol measurement value microgram per liter, microgram per gram 1 Concentration of bishomohopanol 14 microgram per liter false string MIXS:0000175 bishomohopanol +blood_press_diast host blood pressure diastolic measurement value millimeter mercury 1 Resting diastolic blood pressure, measured as mm mercury false string MIXS:0000258 host blood pressure diastolic +blood_press_syst host blood pressure systolic measurement value millimeter mercury 1 Resting systolic blood pressure, measured as mm mercury false string MIXS:0000259 host blood pressure systolic +bromide bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false string MIXS:0000176 bromide build_docs design, construction, and operation documents enumeration 1 The building design, construction and operation documents maintenance plans false build_docs_enum MIXS:0000787 design, construction, and operation documents build_occup_type building occupancy type enumeration m The primary function for which a building or discrete part of a building is intended to be used market true build_occup_type_enum MIXS:0000761 building occupancy type building_setting building setting enumeration 1 A location (geography) where a building is set rural false building_setting_enum MIXS:0000768 building setting built_struc_age built structure age value year 1 The age of the built structure since construction 15 false string MIXS:0000145 built structure age built_struc_set built structure setting enumeration 1 The characterization of the location of the built structure as high or low human density rural false string MIXS:0000778 [urban|rural] built structure setting built_struc_type built structure type free text 1 A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads false string MIXS:0000721 {text} built structure type +calcium calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false string MIXS:0000432 calcium +carb_dioxide carbon dioxide measurement value micromole per liter, parts per million 1 Carbon dioxide (gas) amount or concentration at the time of sampling 410 parts per million false string MIXS:0000097 carbon dioxide +carb_monoxide carbon monoxide measurement value micromole per liter, parts per million 1 Carbon monoxide (gas) amount or concentration at the time of sampling 0.1 parts per million false string MIXS:0000098 carbon monoxide +carb_nitro_ratio carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false string MIXS:0000310 carbon/nitrogen ratio ceil_area ceiling area measurement value square meter 1 The area of the ceiling space within the room 25 square meter false string MIXS:0000148 ceiling area ceil_cond ceiling condition enumeration 1 The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas damaged false ceil_cond_enum MIXS:0000779 ceiling condition ceil_finish_mat ceiling finish material enumeration 1 The type of material used to finish a ceiling stucco false ceil_finish_mat_enum MIXS:0000780 ceiling finish material @@ -157,9 +97,58 @@ ceil_texture ceiling texture enumeration 1 The feel, appearance, or consiste ceil_thermal_mass ceiling thermal mass measurement value joule per degree Celsius 1 The 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 false string MIXS:0000143 ceiling thermal mass ceil_type ceiling type enumeration 1 The type of ceiling according to the ceiling's appearance or construction coffered false ceil_type_enum MIXS:0000784 ceiling type ceil_water_mold ceiling signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the ceiling presence of mold visible false string MIXS:0000781 [presence of mold visible|no presence of mold visible] ceiling signs of water/mold +chem_administration chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11T20:00Z false string MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration +chem_mutagen chemical mutagen mutagen name;mutagen amount;treatment interval and duration milligram per liter m Treatment 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 nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000555 {text};{float} {unit};{Rn/start_time/end_time/duration} chemical mutagen +chem_oxygen_dem chemical oxygen demand measurement value milligram per liter 1 A 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 false string MIXS:0000656 chemical oxygen demand +chem_treat_method chemical treatment method measurement value;frequency;duration;duration milligram per liter 1 Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) false string MIXS:0000457 {float} {unit};{Rn/start_time/end_time/duration};{duration};{duration} chemical treatment method +chem_treatment chemical treatment name;name;timestamp 1 List 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 ACCENT 1125;DOW;2010-11-17 false string MIXS:0001012 {text};{text};{timestamp} chemical treatment +chloride chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false string MIXS:0000429 chloride +chlorophyll chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false string MIXS:0000177 chlorophyll +climate_environment climate environment climate name;treatment interval and duration m Treatment 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 tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment +collection_date collection date date and time The 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 2018-05-11T10:00:00+01:00; 2018-05-11 false string MIXS:0000011 collection date +collection_date_inc Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was harvested/collected/ended. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only true {date, arbitrary precision} incubation collection date +collection_time Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} collection time, GMT +collection_time_inc Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was harvested/collected/ended. Only relevant for incubation samples. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} incubation collection time, GMT +conduc conductivity measurement value milliSiemens per centimeter 1 Electrical conductivity of water 10 milliSiemens per centimeter false string MIXS:0000692 conductivity cool_syst_id cooling system identifier unique identifier 1 The cooling system identifier 12345 false string MIXS:0000785 cooling system identifier +crop_rotation history/crop rotation crop rotation status;schedule 1 Whether or not crop is rotated, and if yes, rotation schedule yes;R2/2017-01-01/2018-12-31/P6M false string MIXS:0000318 {boolean};{Rn/start_time/end_time/duration} history/crop rotation +cult_root_med culture rooting medium name, PMID,DOI or url 1 Name 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. http://himedialabs.com/TD/PT158.pdf false string MIXS:0001041 {text}|{PMID}|{DOI}|{URL} culture rooting medium +cur_land_use current land use enumeration 1 Present state of sample site conifers false cur_land_use_enum MIXS:0001080 current land use +cur_vegetation current vegetation current vegetation type 1 Vegetation classification from one or more standard classification systems, or agricultural crop false string MIXS:0000312 {text} current vegetation +cur_vegetation_meth current vegetation method PMID,DOI or url 1 Reference or method used in vegetation classification false string MIXS:0000314 {PMID}|{DOI}|{URL} current vegetation method date_last_rain date last rain timestamp 1 The date of the last time it rained 2018-05-11:T14:30Z false string MIXS:0000786 date last rain +density density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false string MIXS:0000435 density +depos_env depositional environment enumeration 1 "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If ""other"" is specified, please propose entry in ""additional info"" field" Continental - Alluvial false depos_env_enum MIXS:0000992 depositional environment +depth depth measurement value The 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. 10 meter false string MIXS:0000018 depth dew_point dew point measurement value degree Celsius 1 The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. 22 degree Celsius false string MIXS:0000129 dew point +diether_lipids diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false string MIXS:0000178 {text};{float} {unit} diether lipids +diss_carb_dioxide dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false string MIXS:0000436 dissolved carbon dioxide +diss_hydrogen dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false string MIXS:0000179 dissolved hydrogen +diss_inorg_carb dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false string MIXS:0000434 dissolved inorganic carbon +diss_inorg_nitro dissolved inorganic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of dissolved inorganic nitrogen 761 micromole per liter false string MIXS:0000698 dissolved inorganic nitrogen +diss_inorg_phosp dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false string MIXS:0000106 dissolved inorganic phosphorus +diss_iron dissolved iron measurement value milligram per liter 1 Concentration of dissolved iron in the sample false string MIXS:0000139 dissolved iron +diss_org_carb dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false string MIXS:0000433 dissolved organic carbon +diss_org_nitro dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false string MIXS:0000162 dissolved organic nitrogen +diss_oxygen dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false string MIXS:0000119 dissolved oxygen +diss_oxygen_fluid dissolved oxygen in fluids measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). false string MIXS:0000438 dissolved oxygen in fluids +dna_absorb1 Recommended value is between 1 and 3. 260/280 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/280 +dna_absorb2 Recommended value is between 1 and 3. 260/230 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/230 +dna_concentration Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 2000 0 float true {float} DNA concentration in ng/ul +dna_cont_type Tube or plate (96-well) plate dna_cont_type_enum true DNA container type +dna_cont_well Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ true {96 well plate pos} DNA plate position +dna_container_id Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 true {text < 20 characters} DNA container label +dna_dnase Note DNase treatment is required for all RNA samples. no YesNoEnum true DNase treatment DNA +dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction true {text} DNA isolation method +dna_project_contact Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones true {text} DNA seq project contact +dna_samp_id Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 true {text} DNA sample ID Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled? +dna_sample_format Solution in which the DNA sample has been suspended Water dna_sample_format_enum true DNA sample format +dna_sample_name Give 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. JGI_pond_041618 true {text} DNA sample name +dna_seq_project Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 true {text} DNA seq project ID +dna_seq_project_name Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metagenomics true {text} DNA seq project name +dna_seq_project_pi Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson true {text} DNA seq project PI +dna_volume Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 1000 0 float true {float} DNA volume in ul +dnase_rna Note DNase treatment is required for all RNA samples. no YesNoEnum true DNase treated door_comp_type door type, composite enumeration 1 The composite type of the door revolving false door_comp_type_enum MIXS:0000795 door type, composite door_cond door condition enumeration 1 The phsical condition of the door new false door_cond_enum MIXS:0000788 door condition door_direct door direction of opening enumeration 1 The direction the door opens inward false door_direct_enum MIXS:0000789 door direction of opening @@ -171,16 +160,40 @@ door_type door type enumeration 1 The type of door material wooden fals door_type_metal door type, metal enumeration 1 The type of metal door hollow false door_type_metal_enum MIXS:0000796 door type, metal door_type_wood door type, wood enumeration 1 The type of wood door battened false door_type_wood_enum MIXS:0000797 door type, wood door_water_mold door signs of water/mold enumeration 1 Signs of the presence of mold or mildew on a door presence of mold visible false string MIXS:0000793 [presence of mold visible|no presence of mold visible] door signs of water/mold +down_par downward PAR measurement value microEinstein per square meter per second, microEinstein per square centimeter per second 1 Visible waveband radiance and irradiance measurements in the water column 28.71 microEinstein per square meter per second false string MIXS:0000703 downward PAR +drainage_class drainage classification enumeration 1 Drainage classification from a standard system such as the USDA system well false drainage_class_enum MIXS:0001085 drainage classification drawings drawings enumeration 1 The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents sketch false drawings_enum MIXS:0000798 drawings +ecosystem The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. +ecosystem_category The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. +ecosystem_subtype Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. +ecosystem_type The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. +efficiency_percent efficiency percent measurement value micromole per liter 1 Percentage of volatile solids removed from the anaerobic digestor false string MIXS:0000657 efficiency percent +elev elevation measurement value Elevation 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. 100 meter false string MIXS:0000093 elevation elevator elevator count value 1 The number of elevators within the built structure 2 false string MIXS:0000799 elevator count +emsl_store_temp Enter a temperature in celsius. Numeric portion only. The temperature at which the sample should be stored upon delivery to EMSL -80 true {float} EMSL sample storage temperature, deg. C add 'see_alsos' with link to NEXUS info +emulsions emulsions emulsion name;measurement value gram per liter m Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types false string MIXS:0000660 {text};{float} {unit} emulsions +env_broad_scale broad-scale environmental context The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes. Report 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’s 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 oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean false string MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale local environmental context Environmental entities having causal influences upon the entity at time of sampling. Report the entity or entities which are in the sample or specimen’s 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. litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. false string MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium environmental medium The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Report 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). soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005] false string MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package environmental package MIxS 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 mixs extension false string escalator escalator count value 1 The number of escalators within the built structure 4 false string MIXS:0000800 escalator count +ethylbenzene ethylbenzene measurement value milligram per liter, parts per million 1 Concentration of ethylbenzene in the sample false string MIXS:0000155 ethylbenzene exp_duct exposed ductwork measurement value square meter 1 The amount of exposed ductwork in the room false string MIXS:0000144 exposed ductwork exp_pipe exposed pipes measurement value 1 The number of exposed pipes in the room false string MIXS:0000220 exposed pipes +experimental_factor experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +experimental_factor_other This slot accepts open-ended text about your sample.|We recommend using key:value pairs.|Provided pairs will be considered for inclusion as future slots/terms in this data collection template. Other details about your sample that you feel can't be accurately represented in the available columns. experimental treatment: value true {text} experimental factor- other ext_door exterior door count value 1 The number of exterior doors in the built structure false string MIXS:0000170 exterior door count ext_wall_orient orientations of exterior wall enumeration 1 The orientation of the exterior wall northwest false ext_wall_orient_enum MIXS:0000817 orientations of exterior wall ext_window_orient orientations of exterior window enumeration 1 The compass direction the exterior window of the room is facing southwest false ext_window_orient_enum MIXS:0000818 orientations of exterior window +extreme_event history/extreme events date 1 Unusual physical events that may have affected microbial populations false string MIXS:0000320 history/extreme events +fao_class soil_taxonomic/FAO classification enumeration 1 Soil 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 Luvisols false fao_class_enum MIXS:0001083 soil_taxonomic/FAO classification +fertilizer_regm fertilizer regimen fertilizer name;fertilizer amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000556 {text};{float} {unit};{Rn/start_time/end_time/duration} fertilizer regimen +field field name name 1 Name of the hydrocarbon field (e.g. Albacora) false string MIXS:0000291 {text} field name +filter_method describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci true {text} filter method filter_type filter type enumeration m A device which removes solid particulates or airborne molecular contaminants HEPA true filter_type_enum MIXS:0000765 filter type +fire history/fire date 1 Historical and/or physical evidence of fire false string MIXS:0001086 history/fire fireplace_type fireplace type enumeration 1 A firebox with chimney wood burning false string MIXS:0000802 [gas burning|wood burning] fireplace type +flooding history/flooding date 1 Historical and/or physical evidence of flooding false string MIXS:0000319 history/flooding floor_age floor age value years, weeks, days 1 The time period since installment of the carpet or flooring false string MIXS:0000164 floor age floor_area floor area measurement value square meter 1 The area of the floor space within the room false string MIXS:0000165 floor area floor_cond floor condition enumeration 1 The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas new false floor_cond_enum MIXS:0000803 floor condition @@ -189,160 +202,210 @@ floor_finish_mat floor finish material enumeration 1 The floor covering type floor_struc floor structure enumeration 1 Refers to the structural elements and subfloor upon which the finish flooring is installed concrete false floor_struc_enum MIXS:0000806 floor structure floor_thermal_mass floor thermal mass measurement value joule per degree Celsius 1 The ability of the floor to provide inertia against temperature fluctuations false string MIXS:0000166 floor thermal mass floor_water_mold floor signs of water/mold enumeration 1 Signs of the presence of mold or mildew in a room ceiling discoloration false floor_water_mold_enum MIXS:0000805 floor signs of water/mold +fluor fluorescence measurement value milligram chlorophyll a per cubic meter, volts 1 Raw or converted fluorescence of water 2.5 volts false string MIXS:0000704 fluorescence freq_clean frequency of cleaning enumeration or {text} 1 The number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually. false string MIXS:0000226 frequency of cleaning freq_cook frequency of cooking measurement value 1 The number of times a meal is cooked per week false string MIXS:0000227 frequency of cooking +fungicide_regm fungicide regimen fungicide name;fungicide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000557 {text};{float} {unit};{Rn/start_time/end_time/duration} fungicide regimen furniture furniture enumeration 1 The types of furniture present in the sampled room chair false furniture_enum MIXS:0000807 furniture +gaseous_environment gaseous environment gaseous compound name;gaseous compound amount;treatment interval and duration micromole per liter m Use 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 nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment +gaseous_substances gaseous substances gaseous substance name;measurement value micromole per liter m Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances false string MIXS:0000661 {text};{float} {unit} gaseous substances gender_restroom gender of restroom enumeration 1 The gender type of the restroom male false gender_restroom_enum MIXS:0000808 gender of restroom +genetic_mod genetic modification PMID,DOI,url or free text 1 Genetic 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 aox1A transgenic false string MIXS:0000859 {PMID}|{DOI}|{URL}|{text} genetic modification +geo_loc_name geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The 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) USA: Maryland, Bethesda false string MIXS:0000010 {term}: {term}, {text} geographic location (country and/or sea,region) +glucosidase_act glucosidase activity measurement value mol per liter per hour 1 Measurement of glucosidase activity 5 mol per liter per hour false string MIXS:0000137 glucosidase activity +gravidity gravidity gravidity status;timestamp 1 Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used yes;due date:2018-05-11 false string MIXS:0000875 {boolean};{timestamp} gravidity +gravity gravity gravity factor value;treatment interval and duration meter per square second, g m Information 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 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000559 {float} {unit};{Rn/start_time/end_time/duration} gravity +growth_facil growth facility free text or CO 1 Type 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 Growth chamber [CO_715:0000189] false string MIXS:0001043 {text}|{termLabel} {[termID]} growth facility +growth_habit growth habit enumeration 1 Characteristic shape, appearance or growth form of a plant species spreading false growth_habit_enum MIXS:0001044 growth habit +growth_hormone_regm growth hormone regimen growth hormone name;growth hormone amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000560 {text};{float} {unit};{Rn/start_time/end_time/duration} growth hormone regimen hall_count hallway/corridor count value 1 The total count of hallways and cooridors in the built structure false string MIXS:0000228 hallway/corridor count handidness handidness enumeration 1 The handidness of the individual sampled right handedness false handidness_enum MIXS:0000809 handidness +hc_produced hydrocarbon type produced enumeration 1 "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If ""other"" is specified, please propose entry in ""additional info"" field" Gas false hc_produced_enum MIXS:0000989 hydrocarbon type produced +hcr hydrocarbon resource type enumeration 1 "Main 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" Oil Sand false hcr_enum MIXS:0000988 hydrocarbon resource type +hcr_fw_salinity formation water salinity measurement value milligram per liter 1 Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS false string MIXS:0000406 formation water salinity +hcr_geol_age hydrocarbon resource geological age enumeration 1 "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false hcr_geol_age_enum MIXS:0000993 hydrocarbon resource geological age +hcr_pressure hydrocarbon resource original pressure measurement value range atmosphere, kilopascal 1 Original pressure of the hydrocarbon resource false string MIXS:0000395 {float} - {float} {unit} hydrocarbon resource original pressure +hcr_temp hydrocarbon resource original temperature measurement value range degree Celsius 1 Original temperature of the hydrocarbon resource 150-295 degree Celsius false string MIXS:0000393 {float} - {float} {unit} hydrocarbon resource original temperature heat_cool_type heating and cooling system type enumeration m Methods of conditioning or heating a room or building heat pump true heat_cool_type_enum MIXS:0000766 heating and cooling system type heat_deliv_loc heating delivery locations enumeration 1 The location of heat delivery within the room north false heat_deliv_loc_enum MIXS:0000810 heating delivery locations heat_sys_deliv_meth heating system delivery method enumeration 1 The method by which the heat is delivered through the system radiant false string MIXS:0000812 [conductive|radiant] heating system delivery method heat_system_id heating system identifier unique identifier 1 The heating system identifier false string MIXS:0000833 heating system identifier +heavy_metals extreme_unusual_properties/heavy metals heavy metal name;measurement value unit microgram per gram m Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field. mercury;0.09 micrograms per gram false string MIXS:0000652 {text};{float} {unit} extreme_unusual_properties/heavy metals +heavy_metals_meth extreme_unusual_properties/heavy metals method PMID,DOI or url 1 Reference or method used in determining heavy metals false string MIXS:0000343 {PMID}|{DOI}|{URL} extreme_unusual_properties/heavy metals method height_carper_fiber height carpet fiber mat value centimeter 1 The average carpet fiber height in the indoor environment false string MIXS:0000167 height carpet fiber mat -indoor_space indoor space enumeration 1 A distinguishable space within a structure, the purpose for which discrete areas of a building is used foyer false indoor_space_enum MIXS:0000763 indoor space -indoor_surf indoor surface enumeration 1 Type of indoor surface wall false indoor_surf_enum MIXS:0000764 indoor surface -inside_lux inside lux light measurement value kilowatt per square metre 1 The recorded value at sampling time (power density) false string MIXS:0000168 inside lux light -int_wall_cond interior wall condition enumeration 1 The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas damaged false int_wall_cond_enum MIXS:0000813 interior wall condition -last_clean last time swept/mopped/vacuumed timestamp 1 The last time the floor was cleaned (swept, mopped, vacuumed) 2018-05-11:T14:30Z false string MIXS:0000814 last time swept/mopped/vacuumed -light_type light type enumeration m Application 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 desk lamp true light_type_enum MIXS:0000769 light type -max_occup maximum occupancy measurement value 1 The maximum amount of people allowed in the indoor environment false string MIXS:0000229 maximum occupancy -mech_struc mechanical structure enumeration 1 mechanical structure: a moving structure elevator false mech_struc_enum MIXS:0000815 mechanical structure -number_pets number of pets measurement value 1 The number of pets residing in the sampled space false string MIXS:0000231 number of pets -number_plants number of houseplants measurement value 1 The number of plant(s) in the sampling space false string MIXS:0000230 number of houseplants -number_resident number of residents measurement value 1 The number of individuals currently occupying in the sampling location false string MIXS:0000232 number of residents -occup_density_samp occupant density at sampling measurement value 1 Average number of occupants at time of sampling per square footage false string MIXS:0000217 occupant density at sampling -occup_document occupancy documentation enumeration 1 The type of documentation of occupancy estimate false occup_document_enum MIXS:0000816 occupancy documentation -occup_samp occupancy at sampling measurement value 1 Number of occupants present at time of sample within the given space 10 false string MIXS:0000772 occupancy at sampling -pres_animal_insect presence of pets, animals, or insects enumeration;count 1 The type and number of animals or insects present in the sampling space. cat;5 false ^(cat|dog|rodent|snake|other);\d+$ string MIXS:0000819 presence of pets, animals, or insects -quad_pos quadrant position enumeration 1 The quadrant position of the sampling room within the building West side false quad_pos_enum MIXS:0000820 quadrant position -rel_air_humidity relative air humidity measurement value percentage 1 Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air 80% false string MIXS:0000121 relative air humidity -rel_humidity_out outside relative humidity measurement value gram of air, kilogram of air 1 The recorded outside relative humidity value at the time of sampling 12 per kilogram of air false string MIXS:0000188 outside relative humidity -rel_samp_loc relative sampling location enumeration 1 The sampling location within the train car center of car false rel_samp_loc_enum MIXS:0000821 relative sampling location -room_air_exch_rate room air exchange rate measurement value liter per hour 1 The rate at which outside air replaces indoor air in a given space false string MIXS:0000169 room air exchange rate -room_architec_elem room architectural elements free text 1 The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure false string MIXS:0000233 {text} room architectural elements -room_condt room condition enumeration 1 The condition of the room at the time of sampling new false room_condt_enum MIXS:0000822 room condition -room_connected rooms connected by a doorway enumeration 1 List of rooms connected to the sampling room by a doorway office false room_connected_enum MIXS:0000826 rooms connected by a doorway -room_count room count value 1 The total count of rooms in the built structure including all room types false string MIXS:0000234 room count -room_dim room dimensions measurement value meter 1 The length, width and height of sampling room false string MIXS:0000192 {integer} {unit} x {integer} {unit} x {integer} {unit} room dimensions -room_door_dist room door distance measurement value meter 1 Distance between doors (meters) in the hallway between the sampling room and adjacent rooms false string MIXS:0000193 {integer} {unit} room door distance -room_door_share rooms that share a door with sampling room room name;room number 1 List of room(s) (room number, room name) sharing a door with the sampling room false string MIXS:0000242 {text};{integer} rooms that share a door with sampling room -room_hallway rooms that are on the same hallway room name;room number 1 List of room(s) (room number, room name) located in the same hallway as sampling room false string MIXS:0000238 {text};{integer} rooms that are on the same hallway -room_loc room location in building enumeration 1 The position of the room within the building interior room false room_loc_enum MIXS:0000823 room location in building -room_moist_dam_hist room moisture damage or mold history value 1 The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed false integer MIXS:0000235 room moisture damage or mold history -room_net_area room net area measurement value square feet, square meter 1 The net floor area of sampling room. Net area excludes wall thicknesses false string MIXS:0000194 {integer} {unit} room net area -room_occup room occupancy measurement value 1 Count of room occupancy at time of sampling false string MIXS:0000236 room occupancy -room_samp_pos room sampling position enumeration 1 The horizontal sampling position in the room relative to architectural elements south corner false room_samp_pos_enum MIXS:0000824 room sampling position -room_type room type enumeration 1 The main purpose or activity of the sampling room. A room is any distinguishable space within a structure bathroom false room_type_enum MIXS:0000825 room type -room_vol room volume measurement value cubic feet, cubic meter 1 Volume of sampling room false string MIXS:0000195 {integer} {unit} room volume -room_wall_share rooms that share a wall with sampling room room name;room number 1 List of room(s) (room number, room name) sharing a wall with the sampling room false string MIXS:0000243 {text};{integer} rooms that share a wall with sampling room -room_window_count room window count value 1 Number of windows in the room false integer MIXS:0000237 room window count -samp_floor sampling floor enumeration 1 The floor of the building, where the sampling room is located 4th floor false samp_floor_enum MIXS:0000828 sampling floor -samp_room_id sampling room ID or name value 1 Sampling room number. This ID should be consistent with the designations on the building floor plans false string MIXS:0000244 sampling room ID or name -samp_sort_meth sample size sorting method description of method m Method 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. false string MIXS:0000216 {text} sample size sorting method -samp_time_out sampling time outside time hour 1 The recent and long term history of outside sampling false string MIXS:0000196 sampling time outside -samp_weather sampling day weather enumeration 1 The weather on the sampling day foggy false samp_weather_enum MIXS:0000827 sampling day weather -season season NCIT:C94729 1 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). autumn [NCIT:C94733] false string MIXS:0000829 {termLabel} {[termID]} season -season_use seasonal use enumeration 1 The seasons the space is occupied Winter false season_use_enum MIXS:0000830 seasonal use -shad_dev_water_mold shading device signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the shading device no presence of mold visible false string MIXS:0000834 [presence of mold visible|no presence of mold visible] shading device signs of water/mold -shading_device_cond shading device condition enumeration 1 The physical condition of the shading device at the time of sampling new false shading_device_cond_enum MIXS:0000831 shading device condition -shading_device_loc shading device location enumeration 1 The location of the shading device in relation to the built structure exterior false string MIXS:0000832 [exterior|interior] shading device location -shading_device_mat shading device material material name 1 The material the shading device is composed of false string MIXS:0000245 {text} shading device material -shading_device_type shading device type enumeration 1 The type of shading device slatted aluminum awning false shading_device_type_enum MIXS:0000835 shading device type -space_typ_state space typical state enumeration 1 Customary or normal state of the space typically occupied false string MIXS:0000770 [typically occupied|typically unoccupied] space typical state -specific specifications enumeration 1 The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents construction false specific_enum MIXS:0000836 specifications -specific_humidity specific humidity measurement value gram of air, kilogram of air 1 The 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. 15 per kilogram of air false string MIXS:0000214 specific humidity -substructure_type substructure type enumeration m The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level basement true substructure_type_enum MIXS:0000767 substructure type -surf_air_cont surface-air contaminant enumeration m Contaminant identified on surface radon true surf_air_cont_enum MIXS:0000759 surface-air contaminant -surf_humidity surface humidity measurement value percentage 1 Surfaces: water activity as a function of air and material moisture 10% false string MIXS:0000123 surface humidity -surf_material surface material enumeration 1 Surface materials at the point of sampling wood false surf_material_enum MIXS:0000758 surface material -surf_moisture surface moisture measurement value parts per million, gram per cubic meter, gram per square meter 1 Water held on a surface 0.01 gram per square meter false string MIXS:0000128 surface moisture -surf_moisture_ph surface moisture pH measurement value 1 ph measurement of surface 7 false double MIXS:0000760 surface moisture pH -surf_temp surface temperature measurement value degree Celsius 1 Temperature of the surface at the time of sampling 15 degree Celsius false string MIXS:0000125 surface temperature -temp_out temperature outside house measurement value degree Celsius 1 The recorded temperature value at sampling time outside 5 degree Celsius false string MIXS:0000197 temperature outside house -train_line train line enumeration 1 The subway line name red false train_line_enum MIXS:0000837 train line -train_stat_loc train station collection location enumeration 1 The train station collection location forest hills false train_stat_loc_enum MIXS:0000838 train station collection location -train_stop_loc train stop collection location enumeration 1 The train stop collection location end false train_stop_loc_enum MIXS:0000839 train stop collection location -typ_occup_density typical occupant density measurement value 1 Customary or normal density of occupants 25 false double MIXS:0000771 typical occupant density -vis_media visual media enumeration 1 The building visual media 3D scans false vis_media_enum MIXS:0000840 visual media -wall_area wall area measurement value square meter 1 The total area of the sampled room's walls false string MIXS:0000198 wall area -wall_const_type wall construction type enumeration 1 The building class of the wall defined by the composition of the building elements and fire-resistance rating. fire resistive false wall_const_type_enum MIXS:0000841 wall construction type -wall_finish_mat wall finish material enumeration 1 The material utilized to finish the outer most layer of the wall wood false wall_finish_mat_enum MIXS:0000842 wall finish material -wall_height wall height value centimeter 1 The average height of the walls in the sampled room false string MIXS:0000221 wall height -wall_loc wall location enumeration 1 The relative location of the wall within the room north false wall_loc_enum MIXS:0000843 wall location -wall_surf_treatment wall surface treatment enumeration 1 The surface treatment of interior wall paneling false wall_surf_treatment_enum MIXS:0000845 wall surface treatment -wall_texture wall texture enumeration 1 The feel, appearance, or consistency of a wall surface popcorn false wall_texture_enum MIXS:0000846 wall texture -wall_thermal_mass wall thermal mass measurement value joule per degree Celsius 1 The 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 false string MIXS:0000222 wall thermal mass -wall_water_mold wall signs of water/mold enumeration 1 Signs of the presence of mold or mildew on a wall no presence of mold visible false string MIXS:0000844 [presence of mold visible|no presence of mold visible] wall signs of water/mold -water_feat_size water feature size measurement value square meter 1 The size of the water feature false string MIXS:0000223 water feature size -water_feat_type water feature type enumeration 1 The type of water feature present within the building being sampled stream false water_feat_type_enum MIXS:0000847 water feature type -weekday weekday enumeration 1 The day of the week when sampling occurred Sunday false weekday_enum MIXS:0000848 weekday -window_cond window condition enumeration 1 The physical condition of the window at the time of sampling rupture false window_cond_enum MIXS:0000849 window condition -window_cover window covering enumeration 1 The type of window covering curtains false window_cover_enum MIXS:0000850 window covering -window_horiz_pos window horizontal position enumeration 1 The horizontal position of the window on the wall middle false window_horiz_pos_enum MIXS:0000851 window horizontal position -window_loc window location enumeration 1 The relative location of the window within the room west false window_loc_enum MIXS:0000852 window location -window_mat window material enumeration 1 The type of material used to finish a window wood false window_mat_enum MIXS:0000853 window material -window_open_freq window open frequency value 1 The number of times windows are opened per week false string MIXS:0000246 window open frequency -window_size window area/size measurement value inch, meter 1 The window's length and width false string MIXS:0000224 {float} {unit} x {float} {unit} window area/size -window_status window status enumeration 1 Defines whether the windows were open or closed during environmental testing open false string MIXS:0000855 [closed|open] window status -window_type window type enumeration 1 The type of windows fixed window false window_type_enum MIXS:0000856 window type -window_vert_pos window vertical position enumeration 1 The vertical position of the window on the wall middle false window_vert_pos_enum MIXS:0000857 window vertical position -window_water_mold window signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the window. no presence of mold visible false string MIXS:0000854 [presence of mold visible|no presence of mold visible] window signs of water/mold -alkalinity_method alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method -atmospheric_data atmospheric data atmospheric data name;measurement value m Measurement of atmospheric data; can include multiple data wind speed;9 knots false string MIXS:0001097 {text};{float} {unit} atmospheric data -bac_prod bacterial production measurement value milligram per cubic meter per day 1 Bacterial production in the water column measured by isotope uptake 5 milligram per cubic meter per day false string MIXS:0000683 bacterial production -bac_resp bacterial respiration measurement value milligram per cubic meter per day, micromole oxygen per liter per hour 1 Measurement of bacterial respiration in the water column 300 micromole oxygen per liter per hour false string MIXS:0000684 bacterial respiration -conduc conductivity measurement value milliSiemens per centimeter 1 Electrical conductivity of water 10 milliSiemens per centimeter false string MIXS:0000692 conductivity -diss_inorg_nitro dissolved inorganic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of dissolved inorganic nitrogen 761 micromole per liter false string MIXS:0000698 dissolved inorganic nitrogen -diss_inorg_phosp dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false string MIXS:0000106 dissolved inorganic phosphorus -down_par downward PAR measurement value microEinstein per square meter per second, microEinstein per square centimeter per second 1 Visible waveband radiance and irradiance measurements in the water column 28.71 microEinstein per square meter per second false string MIXS:0000703 downward PAR -fluor fluorescence measurement value milligram chlorophyll a per cubic meter, volts 1 Raw or converted fluorescence of water 2.5 volts false string MIXS:0000704 fluorescence -light_intensity light intensity measurement value lux 1 Measurement of light intensity 0.3 lux false string MIXS:0000706 light intensity -part_org_nitro particulate organic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of particulate organic nitrogen 0.3 micromole per liter false string MIXS:0000719 particulate organic nitrogen -photon_flux photon flux measurement value number of photons per second per unit area 1 Measurement of photon flux 3.926 micromole photons per second per square meter false string MIXS:0000725 photon flux -primary_prod primary production measurement value milligram per cubic meter per day, gram per square meter per day 1 Measurement of primary production, generally measured as isotope uptake 100 milligram per cubic meter per day false string MIXS:0000728 primary production -soluble_react_phosp soluble reactive phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of soluble reactive phosphorus 0.1 milligram per liter false string MIXS:0000738 soluble reactive phosphorus -suspend_part_matter suspended particulate matter measurement value milligram per liter 1 Concentration of suspended particulate matter 0.5 milligram per liter false string MIXS:0000741 suspended particulate matter -tot_diss_nitro total dissolved nitrogen measurement value microgram per liter 1 Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen 40 microgram per liter false string MIXS:0000744 total dissolved nitrogen -tot_inorg_nitro total inorganic nitrogen measurement value microgram per liter 1 Total inorganic nitrogen content 40 microgram per liter false string MIXS:0000745 total inorganic nitrogen -tot_part_carb total particulate carbon measurement value microgram per liter, micromole per liter 1 Total particulate carbon content 35 micromole per liter false string MIXS:0000747 total particulate carbon -water_current water current measurement value cubic meter per second, knots 1 Measurement of magnitude and direction of flow within a fluid 10 cubic meter per second false string MIXS:0000203 water current -ances_data ancestral data free text 1 Information 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) A/3*B false string MIXS:0000247 {text} ancestral data -antibiotic_regm antibiotic regimen antibiotic name;antibiotic amount;treatment interval and duration milligram m Information 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 penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000553 {text};{float} {unit};{Rn/start_time/end_time/duration} antibiotic regimen -biol_stat biological status enumeration 1 The level of genome modification. natural false biol_stat_enum MIXS:0000858 biological status -chem_mutagen chemical mutagen mutagen name;mutagen amount;treatment interval and duration milligram per liter m Treatment 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 nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000555 {text};{float} {unit};{Rn/start_time/end_time/duration} chemical mutagen -cult_root_med culture rooting medium name, PMID,DOI or url 1 Name 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. http://himedialabs.com/TD/PT158.pdf false string MIXS:0001041 {text}|{PMID}|{DOI}|{URL} culture rooting medium -fertilizer_regm fertilizer regimen fertilizer name;fertilizer amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000556 {text};{float} {unit};{Rn/start_time/end_time/duration} fertilizer regimen -fungicide_regm fungicide regimen fungicide name;fungicide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000557 {text};{float} {unit};{Rn/start_time/end_time/duration} fungicide regimen -genetic_mod genetic modification PMID,DOI,url or free text 1 Genetic 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 aox1A transgenic false string MIXS:0000859 {PMID}|{DOI}|{URL}|{text} genetic modification -gravity gravity gravity factor value;treatment interval and duration meter per square second, g m Information 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 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000559 {float} {unit};{Rn/start_time/end_time/duration} gravity -growth_habit growth habit enumeration 1 Characteristic shape, appearance or growth form of a plant species spreading false growth_habit_enum MIXS:0001044 growth habit -growth_hormone_regm growth hormone regimen growth hormone name;growth hormone amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000560 {text};{float} {unit};{Rn/start_time/end_time/duration} growth hormone regimen herbicide_regm herbicide regimen herbicide name;herbicide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000561 {text};{float} {unit};{Rn/start_time/end_time/duration} herbicide regimen +horizon_meth soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} soil horizon method host_age host age value year, day, hour 1 Age 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 10 days false string MIXS:0000255 host age +host_body_habitat host body habitat free text 1 Original body habitat where the sample was obtained from nasopharynx false string MIXS:0000866 {text} host body habitat +host_body_product host body product FMA or UBERON 1 Substance 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 Portion of mucus [fma66938] false string MIXS:0000888 {termLabel} {[termID]} host body product +host_body_site host body site FMA or UBERON 1 Name 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 gill [UBERON:0002535] false string MIXS:0000867 {termLabel} {[termID]} host body site +host_body_temp host body temperature measurement value degree Celsius 1 Core body temperature of the host when sample was collected 15 degree Celsius false string MIXS:0000274 host body temperature +host_color host color color 1 The color of host false string MIXS:0000260 {text} host color host_common_name host common name common name 1 Common name of the host. human false string MIXS:0000248 {text} host common name +host_diet host diet diet type m Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types herbivore false string MIXS:0000869 {text} host diet host_dry_mass host dry mass measurement value kilogram, gram 1 Measurement of dry mass 500 gram false string MIXS:0000257 host dry mass +host_family_relation host family relationship relationship type;arbitrary identifier m Familial relationships to other hosts in the same study; can include multiple relationships offspring;Mussel25 false string MIXS:0000872 {text};{text} host family relationship host_genotype host genotype genotype 1 Observed genotype C57BL/6 false string MIXS:0000365 {text} host genotype +host_growth_cond host growth conditions PMID,DOI,url or free text 1 Literature reference giving growth conditions of the host https://academic.oup.com/icesjms/article/68/2/349/617247 false string MIXS:0000871 {PMID}|{DOI}|{URL}|{text} host growth conditions host_height host height measurement value centimeter, millimeter, meter 1 The height of subject 0.1 meter false string MIXS:0000264 host height +host_last_meal host last meal content;duration m Content of last meal and time since feeding; can include multiple values corn feed;P2H false string MIXS:0000870 {text};{duration} host last meal host_length host length measurement value centimeter, millimeter, meter 1 The length of subject 1 meter false string MIXS:0000256 host length host_life_stage host life stage stage 1 Description of life stage of host adult false string MIXS:0000251 {text} host life stage host_phenotype host phenotype PATO or HP 1 Phenotype 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 elongated [PATO:0001154] false string MIXS:0000874 {termLabel} {[termID]} host phenotype +host_sex host sex enumeration 1 Gender or physical sex of the host. non-binary false host_sex_enum MIXS:0000811 host sex +host_shape host shape shape 1 Morphological shape of host round false string MIXS:0000261 {text} host shape +host_subject_id host subject id unique identifier 1 A unique identifier by which each subject can be referred to, de-identified. MPI123 false string MIXS:0000861 {text} host subject id host_subspecf_genlin host subspecific genetic lineage Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar. m Information 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. serovar:Newport, variety:glabrum, cultivar: Red Delicious false string MIXS:0001318 {rank name}:{text} host subspecific genetic lineage +host_substrate host substrate substrate name 1 The growth substrate of the host. rock false string MIXS:0000252 {text} host substrate host_symbiont observed host symbionts species name or common name m The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. flukeworms false string MIXS:0001298 {text} observed host symbionts host_taxid host taxid NCBI taxon identifier 1 NCBI taxon id of the host, e.g. 9606 7955 false string MIXS:0000250 {NCBI taxid} host taxid host_tot_mass host total mass measurement value kilogram, gram 1 Total mass of the host at collection, the unit depends on host 2500 gram false string MIXS:0000263 host total mass host_wet_mass host wet mass measurement value kilogram, gram 1 Measurement of wet mass 1500 gram false string MIXS:0000567 host wet mass +humidity humidity measurement value gram per cubic meter 1 Amount of water vapour in the air, at the time of sampling 25 gram per cubic meter false string MIXS:0000100 humidity +humidity_regm humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen +indoor_space indoor space enumeration 1 A distinguishable space within a structure, the purpose for which discrete areas of a building is used foyer false indoor_space_enum MIXS:0000763 indoor space +indoor_surf indoor surface enumeration 1 Type of indoor surface wall false indoor_surf_enum MIXS:0000764 indoor surface +indust_eff_percent industrial effluent percent measurement value percentage 1 Percentage of industrial effluents received by wastewater treatment plant false string MIXS:0000662 industrial effluent percent +inorg_particles inorganic particles inorganic particle name;measurement value mole per liter, milligram per liter m Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles false string MIXS:0000664 {text};{float} {unit} inorganic particles +inside_lux inside lux light measurement value kilowatt per square metre 1 The recorded value at sampling time (power density) false string MIXS:0000168 inside lux light +int_wall_cond interior wall condition enumeration 1 The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas damaged false int_wall_cond_enum MIXS:0000813 interior wall condition +isotope_exposure This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? +iw_bt_date_well injection water breakthrough date of specific well timestamp 1 Injection water breakthrough date per well following a secondary and/or tertiary recovery 2018-05-11 false string MIXS:0001010 injection water breakthrough date of specific well +iwf injection water fraction measurement value percent 1 Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) false string MIXS:0000455 injection water fraction +last_clean last time swept/mopped/vacuumed timestamp 1 The last time the floor was cleaned (swept, mopped, vacuumed) 2018-05-11:T14:30Z false string MIXS:0000814 last time swept/mopped/vacuumed +lat_lon geographic location (latitude and longitude) decimal degrees, limit to 8 decimal points The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system 50.586825 6.408977 false string MIXS:0000009 {float} {float} geographic location (latitude and longitude) +lbc_thirty lbc_thirty|lbc30|lime buffer capacity (at 30 minutes) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined after 30 minute incubation 543 mg/kg false string lime buffer capacity (at 30 minutes) +lbceq lbceq|lime buffer capacity (at 5-day equilibrium) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined at equilibrium after 5 day incubation 1575 mg/kg false string lime buffer capacity (after 5 day incubation) +light_intensity light intensity measurement value lux 1 Measurement of light intensity 0.3 lux false string MIXS:0000706 light intensity +light_regm light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false string MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen +light_type light type enumeration m Application 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 desk lamp true light_type_enum MIXS:0000769 light type +link_class_info link to classification information PMID,DOI or url 1 Link to digitized soil maps or other soil classification information false string MIXS:0000329 {PMID}|{DOI}|{URL} link to classification information +link_climate_info link to climate information PMID,DOI or url 1 Link to climate resource false string MIXS:0000328 {PMID}|{DOI}|{URL} link to climate information +lithology lithology enumeration 1 "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If ""other"" is specified, please propose entry in ""additional info"" field" Volcanic false lithology_enum MIXS:0000990 lithology +local_class soil_taxonomic/local classification local classification name 1 Soil classification based on local soil classification system false string MIXS:0000330 {text} soil_taxonomic/local classification +local_class_meth soil_taxonomic/local classification method PMID,DOI or url 1 Reference or method used in determining the local soil classification false string MIXS:0000331 {PMID}|{DOI}|{URL} soil_taxonomic/local classification method +magnesium magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false string MIXS:0000431 magnesium +manganese manganese measurement value mg/kg (ppm) 1 Concentration of manganese in the sample 24.7 mg/kg false string manganese +max_occup maximum occupancy measurement value 1 The maximum amount of people allowed in the indoor environment false string MIXS:0000229 maximum occupancy +mean_frict_vel mean friction velocity measurement value meter per second 1 Measurement of mean friction velocity 0.5 meter per second false string MIXS:0000498 mean friction velocity +mean_peak_frict_vel mean peak friction velocity measurement value meter per second 1 Measurement of mean peak friction velocity 1 meter per second false string MIXS:0000502 mean peak friction velocity +mech_struc mechanical structure enumeration 1 mechanical structure: a moving structure elevator false mech_struc_enum MIXS:0000815 mechanical structure mechanical_damage mechanical damage damage type;body site m Information about any mechanical damage exerted on the plant; can include multiple damages and sites pruning;bark false string MIXS:0001052 {text};{text} mechanical damage +methane methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false string MIXS:0000101 methane +micro_biomass_c_meth "required if ""microbial_biomass_c"" is provided" Reference or method used in determining microbial biomass carbon https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 true {PMID}|{DOI}|{URL} microbial biomass carbon method How should we separate values? | or ;? lets be consistent +micro_biomass_meth microbial biomass method PMID,DOI or url 1 Reference or method used in determining microbial biomass false string MIXS:0000339 {PMID}|{DOI}|{URL} microbial biomass method +micro_biomass_n_meth "required if ""microbial_biomass_n"" is provided" Reference or method used in determining microbial biomass nitrogen https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 {PMID}|{DOI}|{URL} microbial biomass nitrogen method +microbial_biomass microbial biomass measurement value ton, kilogram, gram per kilogram soil 1 The 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 false string MIXS:0000650 microbial biomass +microbial_biomass_c If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil {float} {unit} microbial biomass carbon +microbial_biomass_n If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil {float} {unit} microbial biomass nitrogen mineral_nutr_regm mineral nutrient regimen mineral nutrient name;mineral nutrient amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000570 {text};{float} {unit};{Rn/start_time/end_time/duration} mineral nutrient regimen +misc_param miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +n_alkanes n-alkanes n-alkane name;measurement value micromole per liter m Concentration of n-alkanes; can include multiple n-alkanes n-hexadecane;100 milligram per liter false string MIXS:0000503 {text};{float} {unit} n-alkanes +nitrate nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false string MIXS:0000425 nitrate +nitrate_nitrogen nitrate_nitrogen|NO3-N measurement value mg/kg 1 often below some specified limit of detection Concentration of nitrate nitrogen in the sample 0.29 mg/kg false string nitrate_nitrogen +nitrite nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false string MIXS:0000426 nitrite +nitrite_nitrogen nitrite_nitrogen|NO2-N measurement value mg/kg 1 Concentration of nitrite nitrogen in the sample 1.2 mg/kg false string nitrite_nitrogen +nitro nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false string MIXS:0000504 nitrogen +non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g {text};{float} {unit} non-microbial biomass +non_microb_biomass_method "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 {PMID}|{DOI}|{URL} non-microbial biomass method non_min_nutr_regm non-mineral nutrient regimen non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000571 {text};{float} {unit};{Rn/start_time/end_time/duration} non-mineral nutrient regimen +number_pets number of pets measurement value 1 The number of pets residing in the sampled space false string MIXS:0000231 number of pets +number_plants number of houseplants measurement value 1 The number of plant(s) in the sampling space false string MIXS:0000230 number of houseplants +number_resident number of residents measurement value 1 The number of individuals currently occupying in the sampling location false string MIXS:0000232 number of residents +occup_density_samp occupant density at sampling measurement value 1 Average number of occupants at time of sampling per square footage false string MIXS:0000217 occupant density at sampling +occup_document occupancy documentation enumeration 1 The type of documentation of occupancy estimate false occup_document_enum MIXS:0000816 occupancy documentation +occup_samp occupancy at sampling measurement value 1 Number of occupants present at time of sample within the given space 10 false string MIXS:0000772 occupancy at sampling +org_carb organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false string MIXS:0000508 organic carbon +org_count_qpcr_info organism count qPCR information gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles number of cells per gram (or ml or cm^2) 1 If 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) false string MIXS:0000099 {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles organism count qPCR information +org_matter organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false string MIXS:0000204 organic matter +org_nitro organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false string MIXS:0000205 organic nitrogen +org_nitro_method "required if ""org_nitro"" is provided" Method used for obtaining organic nitrogen https://doi.org/10.1016/0038-0717(85)90144-0 {PMID}|{DOI}|{URL} organic nitrogen method +org_particles organic particles particle name;measurement value gram per liter m Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. false string MIXS:0000665 {text};{float} {unit} organic particles +organism_count organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false string MIXS:0000103 organism count +other_treatment This is an open text field to provide any treatments that cannot be captured in the provided slots. Other treatments applied to your samples that are not applicable to the provided fields true {text} other treatments +owc_tvdss oil water contact depth measurement value meter 1 Depth of the original oil water contact (OWC) zone (average) (m TVDSS) false string MIXS:0000405 oil water contact depth +oxy_stat_samp oxygenation status of sample enumeration 1 Oxygenation status of sample aerobic false rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample +oxygen oxygen measurement value milligram per liter, parts per million 1 Oxygen (gas) amount or concentration at the time of sampling 600 parts per million false string MIXS:0000104 oxygen +part_org_carb particulate organic carbon measurement value microgram per liter 1 Concentration of particulate organic carbon 1.92 micromole per liter false string MIXS:0000515 particulate organic carbon +part_org_nitro particulate organic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of particulate organic nitrogen 0.3 micromole per liter false string MIXS:0000719 particulate organic nitrogen +particle_class particle classification particle name;measurement value micrometer m Particles 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 false string MIXS:0000206 {text};{float} {unit} particle classification +permeability permeability measurement value range mD 1 Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) false string MIXS:0000404 {integer} - {integer} {unit} permeability +perturbation perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation pesticide_regm pesticide regimen pesticide name;pesticide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000573 {text};{float} {unit};{Rn/start_time/end_time/duration} pesticide regimen +petroleum_hydrocarb petroleum hydrocarbon measurement value micromole per liter 1 Concentration of petroleum hydrocarbon 0.05 micromole per liter false string MIXS:0000516 petroleum hydrocarbon +ph pH measurement value 1 Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 false double MIXS:0001001 pH +ph_meth pH method PMID,DOI or url 1 Reference or method used in determining ph false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method ph_regm pH regimen measurement value;treatment interval and duration m Information 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 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001056 {float};{Rn/start_time/end_time/duration} pH regimen +phaeopigments phaeopigments phaeopigment name;measurement value milligram per cubic meter m Concentration of phaeopigments; can include multiple phaeopigments 2.5 milligram per cubic meter false string MIXS:0000180 {text};{float} {unit} phaeopigments +phosphate phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false string MIXS:0000505 phosphate +phosplipid_fatt_acid phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid +photon_flux photon flux measurement value number of photons per second per unit area 1 Measurement of photon flux 3.926 micromole photons per second per square meter false string MIXS:0000725 photon flux plant_growth_med plant growth medium EO or enumeration 1 Specification 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 hydroponic plant culture media [EO:0007067] false string MIXS:0001057 plant growth medium plant_product plant product product name 1 Substance produced by the plant, where the sample was obtained from xylem sap [PO:0025539] false string MIXS:0001058 {text} plant product plant_sex plant sex enumeration 1 Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite. Hermaphroditic false plant_sex_enum MIXS:0001059 plant sex plant_struc plant structure PO 1 Name 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. epidermis [PO:0005679] false string MIXS:0001060 {termLabel} {[termID]} plant structure +pollutants pollutants pollutant name;measurement value gram, mole per liter, milligram per liter, microgram per cubic meter m Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant lead;0.15 microgram per cubic meter false string MIXS:0000107 {text};{float} {unit} pollutants +porosity porosity measurement value or range percentage 1 Porosity of deposited sediment is volume of voids divided by the total volume of sample false string MIXS:0000211 {float} - {float} {unit} porosity +potassium potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false string MIXS:0000430 potassium +pour_point pour point measurement value degree Celsius 1 Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is 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) false string MIXS:0000127 pour point +pre_treatment pre-treatment pre-treatment type 1 The process of pre-treatment removes materials that can be easily collected from the raw wastewater false string MIXS:0000348 {text} pre-treatment +pres_animal_insect presence of pets, animals, or insects enumeration;count 1 The type and number of animals or insects present in the sampling space. cat;5 false ^(cat|dog|rodent|snake|other);\d+$ string MIXS:0000819 presence of pets, animals, or insects +pressure pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false string MIXS:0000412 pressure +prev_land_use_meth history/previous land use method PMID,DOI or url 1 Reference or method used in determining previous land use and dates false string MIXS:0000316 {PMID}|{DOI}|{URL} history/previous land use method +previous_land_use history/previous land use land use name;date 1 Previous land use and dates false string MIXS:0000315 {text};{timestamp} history/previous land use +primary_prod primary production measurement value milligram per cubic meter per day, gram per square meter per day 1 Measurement of primary production, generally measured as isotope uptake 100 milligram per cubic meter per day false string MIXS:0000728 primary production +primary_treatment primary treatment primary treatment type 1 The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed false string MIXS:0000349 {text} primary treatment +prod_rate production rate measurement value cubic meter per day 1 Oil and/or gas production rates per well (e.g. 524 m3 / day) false string MIXS:0000452 production rate +prod_start_date production start date timestamp 1 Date of field's first production 2018-05-11 false string MIXS:0001008 production start date +profile_position profile position enumeration 1 Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas summit false profile_position_enum MIXS:0001084 profile position +project_id Proposal IDs or names associated with dataset true {text} project ID +proposal_dna Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 true {text} DNA proposal ID +proposal_rna Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 true {text} RNA proposal ID +quad_pos quadrant position enumeration 1 The quadrant position of the sampling room within the building West side false quad_pos_enum MIXS:0000820 quadrant position radiation_regm radiation regimen radiation type name;radiation amount;treatment interval and duration rad, gray m Information 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 gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000575 {text};{float} {unit};{Rn/start_time/end_time/duration} radiation regimen rainfall_regm rainfall regimen measurement value;treatment interval and duration millimeter m Information 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 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000576 {float} {unit};{Rn/start_time/end_time/duration} rainfall regimen +reactor_type reactor type reactor type name 1 Anaerobic 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 false string MIXS:0000350 {text} reactor type +redox_potential redox potential measurement value millivolt 1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential 300 millivolt false string MIXS:0000182 redox potential +rel_air_humidity relative air humidity measurement value percentage 1 Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air 80% false string MIXS:0000121 relative air humidity +rel_humidity_out outside relative humidity measurement value gram of air, kilogram of air 1 The recorded outside relative humidity value at the time of sampling 12 per kilogram of air false string MIXS:0000188 outside relative humidity +rel_samp_loc relative sampling location enumeration 1 The sampling location within the train car center of car false rel_samp_loc_enum MIXS:0000821 relative sampling location +rel_to_oxygen relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +replicate_number This will guide staff in ensuring your samples are block & randomized correctly If sending biological replicates, indicate the rep number here. true {integer} replicate number +reservoir reservoir name name 1 Name of the reservoir (e.g. Carapebus) false string MIXS:0000303 {text} reservoir name +resins_pc resins wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000134 {text};{float} {unit} resins wt% +rna_absorb1 Recommended value is between 1 and 3. 260/280 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/280 +rna_absorb2 Recommended value is between 1 and 3. 260/230 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/230 +rna_concentration Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 1000 0 float true {float} RNA concentration in ng/ul +rna_cont_type Tube or plate (96-well) plate rna_cont_type_enum true RNA container type +rna_cont_well Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ true {96 well plate pos} RNA plate position +rna_container_id Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 true {text} RNA container label +rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction true {text} RNA isolation method +rna_project_contact Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones true {text} RNA seq project contact +rna_samp_id Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 true {text} RNA sample ID +rna_sample_format Solution in which the RNA sample has been suspended Water rna_sample_format_enum true RNA sample format +rna_sample_name Give 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. JGI_pond_041618 2000 0 true {text} RNA sample name +rna_seq_project Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 true {text} RNA seq project ID +rna_seq_project_name Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metatranscriptomics true {text} RNA seq project name +rna_seq_project_pi Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson true {text} RNA seq project PI +rna_volume Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 float true {float} RNA volume in ul +room_air_exch_rate room air exchange rate measurement value liter per hour 1 The rate at which outside air replaces indoor air in a given space false string MIXS:0000169 room air exchange rate +room_architec_elem room architectural elements free text 1 The unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure false string MIXS:0000233 {text} room architectural elements +room_condt room condition enumeration 1 The condition of the room at the time of sampling new false room_condt_enum MIXS:0000822 room condition +room_connected rooms connected by a doorway enumeration 1 List of rooms connected to the sampling room by a doorway office false room_connected_enum MIXS:0000826 rooms connected by a doorway +room_count room count value 1 The total count of rooms in the built structure including all room types false string MIXS:0000234 room count +room_dim room dimensions measurement value meter 1 The length, width and height of sampling room false string MIXS:0000192 {integer} {unit} x {integer} {unit} x {integer} {unit} room dimensions +room_door_dist room door distance measurement value meter 1 Distance between doors (meters) in the hallway between the sampling room and adjacent rooms false string MIXS:0000193 {integer} {unit} room door distance +room_door_share rooms that share a door with sampling room room name;room number 1 List of room(s) (room number, room name) sharing a door with the sampling room false string MIXS:0000242 {text};{integer} rooms that share a door with sampling room +room_hallway rooms that are on the same hallway room name;room number 1 List of room(s) (room number, room name) located in the same hallway as sampling room false string MIXS:0000238 {text};{integer} rooms that are on the same hallway +room_loc room location in building enumeration 1 The position of the room within the building interior room false room_loc_enum MIXS:0000823 room location in building +room_moist_dam_hist room moisture damage or mold history value 1 The history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed false integer MIXS:0000235 room moisture damage or mold history +room_net_area room net area measurement value square feet, square meter 1 The net floor area of sampling room. Net area excludes wall thicknesses false string MIXS:0000194 {integer} {unit} room net area +room_occup room occupancy measurement value 1 Count of room occupancy at time of sampling false string MIXS:0000236 room occupancy +room_samp_pos room sampling position enumeration 1 The horizontal sampling position in the room relative to architectural elements south corner false room_samp_pos_enum MIXS:0000824 room sampling position +room_type room type enumeration 1 The main purpose or activity of the sampling room. A room is any distinguishable space within a structure bathroom false room_type_enum MIXS:0000825 room type +room_vol room volume measurement value cubic feet, cubic meter 1 Volume of sampling room false string MIXS:0000195 {integer} {unit} room volume +room_wall_share rooms that share a wall with sampling room room name;room number 1 List of room(s) (room number, room name) sharing a wall with the sampling room false string MIXS:0000243 {text};{integer} rooms that share a wall with sampling room +room_window_count room window count value 1 Number of windows in the room false integer MIXS:0000237 room window count root_cond rooting conditions PMID,DOI,url or free text 1 Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. http://himedialabs.com/TD/PT158.pdf false string MIXS:0001061 {PMID}|{DOI}|{URL}|{text} rooting conditions root_med_carbon rooting medium carbon carbon source name;measurement value milligram per liter 1 Source of organic carbon in the culture rooting medium; e.g. sucrose. sucrose false string MIXS:0000577 {text};{float} {unit} rooting medium carbon root_med_macronutr rooting medium macronutrients macronutrient name;measurement value milligram per liter 1 Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). KH2PO4;170¬†milligram per liter false string MIXS:0000578 {text};{float} {unit} rooting medium macronutrients @@ -351,306 +414,245 @@ root_med_ph rooting medium pH measurement value 1 pH measurement of the cult root_med_regl rooting medium regulators regulator name;measurement value milligram per liter 1 Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. abscisic acid;0.75 milligram per liter false string MIXS:0000581 {text};{float} {unit} rooting medium regulators root_med_solid rooting medium solidifier name 1 Specification of the solidifying agent in the culture rooting medium; e.g. agar. agar false string MIXS:0001063 {text} rooting medium solidifier root_med_suppl rooting medium organic supplements supplement name;measurement value milligram per liter 1 Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). nicotinic acid;0.5 milligram per liter false string MIXS:0000580 {text};{float} {unit} rooting medium organic supplements +salinity salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false string MIXS:0000183 salinity +salinity_meth salinity method PMID,DOI or url 1 Reference or method used in determining salinity false string MIXS:0000341 {PMID}|{DOI}|{URL} salinity method salt_regm salt regimen salt name;salt amount;treatment interval and duration gram, microgram, mole per liter, gram per liter m Information 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 NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000582 {text};{float} {unit};{Rn/start_time/end_time/duration} salt regimen samp_capt_status sample capture status enumeration 1 Reason for the sample farm sample false samp_capt_status_enum MIXS:0000860 sample capture status -samp_dis_stage sample disease stage enumeration 1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. infection false samp_dis_stage_enum MIXS:0000249 sample disease stage -season_environment seasonal environment seasonal environment name;treatment interval and duration m Treatment 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 rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001068 {text};{Rn/start_time/end_time/duration} seasonal environment -size_frac size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -standing_water_regm standing water regimen standing water type;treatment interval and duration m Treatment 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 standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001069 {text};{Rn/start_time/end_time/duration} standing water regimen -tiss_cult_growth_med tissue culture growth media PMID,DOI,url or free text 1 Description of plant tissue culture growth media used https://link.springer.com/content/pdf/10.1007/BF02796489.pdf false string MIXS:0001070 {PMID}|{DOI}|{URL}|{text} tissue culture growth media -water_temp_regm water temperature regimen measurement value;treatment interval and duration degree Celsius m Information 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 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000590 {float} {unit};{Rn/start_time/end_time/duration} water temperature regimen -add_recov_method secondary and tertiary recovery methods and start date enumeration;timestamp 1 "Additional (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" Polymer Addition;2018-06-21T14:30Z false string MIXS:0001009 secondary and tertiary recovery methods and start date -additional_info additional info text 1 Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary false string MIXS:0000300 {text} additional info -api API gravity measurement value degrees API 1 API 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¬∞ API) false string MIXS:0000157 API gravity -aromatics_pc aromatics wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000133 {text};{float} {unit} aromatics wt% -asphaltenes_pc asphaltenes wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000135 {text};{float} {unit} asphaltenes wt% -basin basin name name 1 Name of the basin (e.g. Campos) false string MIXS:0000290 {text} basin name -benzene benzene measurement value milligram per liter, parts per million 1 Concentration of benzene in the sample false string MIXS:0000153 benzene -biochem_oxygen_dem biochemical oxygen demand measurement value milligram per liter 1 Amount 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 false string MIXS:0000653 biochemical oxygen demand -biocide biocide administration name;name;timestamp 1 List of biocides (commercial name of product and supplier) and date of administration ALPHA 1427;Baker Hughes;2008-01-23 false string MIXS:0001011 {text};{text};{timestamp} biocide administration -biocide_admin_method biocide administration method measurement value;frequency;duration;duration milligram per liter 1 Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) false string MIXS:0000456 {float} {unit};{Rn/start_time/end_time/duration};{duration} biocide administration method -blood_press_diast host blood pressure diastolic measurement value millimeter mercury 1 Resting diastolic blood pressure, measured as mm mercury false string MIXS:0000258 host blood pressure diastolic -blood_press_syst host blood pressure systolic measurement value millimeter mercury 1 Resting systolic blood pressure, measured as mm mercury false string MIXS:0000259 host blood pressure systolic -chem_oxygen_dem chemical oxygen demand measurement value milligram per liter 1 A 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 false string MIXS:0000656 chemical oxygen demand -chem_treat_method chemical treatment method measurement value;frequency;duration;duration milligram per liter 1 Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) false string MIXS:0000457 {float} {unit};{Rn/start_time/end_time/duration};{duration};{duration} chemical treatment method -chem_treatment chemical treatment name;name;timestamp 1 List 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 ACCENT 1125;DOW;2010-11-17 false string MIXS:0001012 {text};{text};{timestamp} chemical treatment -depos_env depositional environment enumeration 1 "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If ""other"" is specified, please propose entry in ""additional info"" field" Continental - Alluvial false depos_env_enum MIXS:0000992 depositional environment -diss_iron dissolved iron measurement value milligram per liter 1 Concentration of dissolved iron in the sample false string MIXS:0000139 dissolved iron -diss_oxygen_fluid dissolved oxygen in fluids measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). false string MIXS:0000438 dissolved oxygen in fluids -efficiency_percent efficiency percent measurement value micromole per liter 1 Percentage of volatile solids removed from the anaerobic digestor false string MIXS:0000657 efficiency percent -emulsions emulsions emulsion name;measurement value gram per liter m Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types false string MIXS:0000660 {text};{float} {unit} emulsions -ethylbenzene ethylbenzene measurement value milligram per liter, parts per million 1 Concentration of ethylbenzene in the sample false string MIXS:0000155 ethylbenzene -field field name name 1 Name of the hydrocarbon field (e.g. Albacora) false string MIXS:0000291 {text} field name -gaseous_substances gaseous substances gaseous substance name;measurement value micromole per liter m Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances false string MIXS:0000661 {text};{float} {unit} gaseous substances -gravidity gravidity gravidity status;timestamp 1 Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used yes;due date:2018-05-11 false string MIXS:0000875 {boolean};{timestamp} gravidity -hc_produced hydrocarbon type produced enumeration 1 "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If ""other"" is specified, please propose entry in ""additional info"" field" Gas false hc_produced_enum MIXS:0000989 hydrocarbon type produced -hcr hydrocarbon resource type enumeration 1 "Main 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" Oil Sand false hcr_enum MIXS:0000988 hydrocarbon resource type -hcr_fw_salinity formation water salinity measurement value milligram per liter 1 Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS false string MIXS:0000406 formation water salinity -hcr_geol_age hydrocarbon resource geological age enumeration 1 "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false hcr_geol_age_enum MIXS:0000993 hydrocarbon resource geological age -hcr_pressure hydrocarbon resource original pressure measurement value range atmosphere, kilopascal 1 Original pressure of the hydrocarbon resource false string MIXS:0000395 {float} - {float} {unit} hydrocarbon resource original pressure -hcr_temp hydrocarbon resource original temperature measurement value range degree Celsius 1 Original temperature of the hydrocarbon resource 150-295 degree Celsius false string MIXS:0000393 {float} - {float} {unit} hydrocarbon resource original temperature -host_body_habitat host body habitat free text 1 Original body habitat where the sample was obtained from nasopharynx false string MIXS:0000866 {text} host body habitat -host_body_product host body product FMA or UBERON 1 Substance 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 Portion of mucus [fma66938] false string MIXS:0000888 {termLabel} {[termID]} host body product -host_body_site host body site FMA or UBERON 1 Name 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 gill [UBERON:0002535] false string MIXS:0000867 {termLabel} {[termID]} host body site -host_body_temp host body temperature measurement value degree Celsius 1 Core body temperature of the host when sample was collected 15 degree Celsius false string MIXS:0000274 host body temperature -host_color host color color 1 The color of host false string MIXS:0000260 {text} host color -host_diet host diet diet type m Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types herbivore false string MIXS:0000869 {text} host diet -host_family_relation host family relationship relationship type;arbitrary identifier m Familial relationships to other hosts in the same study; can include multiple relationships offspring;Mussel25 false string MIXS:0000872 {text};{text} host family relationship -host_growth_cond host growth conditions PMID,DOI,url or free text 1 Literature reference giving growth conditions of the host https://academic.oup.com/icesjms/article/68/2/349/617247 false string MIXS:0000871 {PMID}|{DOI}|{URL}|{text} host growth conditions -host_last_meal host last meal content;duration m Content of last meal and time since feeding; can include multiple values corn feed;P2H false string MIXS:0000870 {text};{duration} host last meal -host_sex host sex enumeration 1 Gender or physical sex of the host. non-binary false host_sex_enum MIXS:0000811 host sex -host_shape host shape shape 1 Morphological shape of host round false string MIXS:0000261 {text} host shape -host_subject_id host subject id unique identifier 1 A unique identifier by which each subject can be referred to, de-identified. MPI123 false string MIXS:0000861 {text} host subject id -host_substrate host substrate substrate name 1 The growth substrate of the host. rock false string MIXS:0000252 {text} host substrate -indust_eff_percent industrial effluent percent measurement value percentage 1 Percentage of industrial effluents received by wastewater treatment plant false string MIXS:0000662 industrial effluent percent -inorg_particles inorganic particles inorganic particle name;measurement value mole per liter, milligram per liter m Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles false string MIXS:0000664 {text};{float} {unit} inorganic particles -iw_bt_date_well injection water breakthrough date of specific well timestamp 1 Injection water breakthrough date per well following a secondary and/or tertiary recovery 2018-05-11 false string MIXS:0001010 injection water breakthrough date of specific well -iwf injection water fraction measurement value percent 1 Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) false string MIXS:0000455 injection water fraction -lithology lithology enumeration 1 "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If ""other"" is specified, please propose entry in ""additional info"" field" Volcanic false lithology_enum MIXS:0000990 lithology -org_count_qpcr_info organism count qPCR information gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles number of cells per gram (or ml or cm^2) 1 If 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) false string MIXS:0000099 {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles organism count qPCR information -org_particles organic particles particle name;measurement value gram per liter m Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. false string MIXS:0000665 {text};{float} {unit} organic particles -owc_tvdss oil water contact depth measurement value meter 1 Depth of the original oil water contact (OWC) zone (average) (m TVDSS) false string MIXS:0000405 oil water contact depth -permeability permeability measurement value range mD 1 Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) false string MIXS:0000404 {integer} - {integer} {unit} permeability -pour_point pour point measurement value degree Celsius 1 Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is 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) false string MIXS:0000127 pour point -pre_treatment pre-treatment pre-treatment type 1 The process of pre-treatment removes materials that can be easily collected from the raw wastewater false string MIXS:0000348 {text} pre-treatment -primary_treatment primary treatment primary treatment type 1 The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed false string MIXS:0000349 {text} primary treatment -prod_rate production rate measurement value cubic meter per day 1 Oil and/or gas production rates per well (e.g. 524 m3 / day) false string MIXS:0000452 production rate -prod_start_date production start date timestamp 1 Date of field's first production 2018-05-11 false string MIXS:0001008 production start date -reactor_type reactor type reactor type name 1 Anaerobic 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 false string MIXS:0000350 {text} reactor type -reservoir reservoir name name 1 Name of the reservoir (e.g. Carapebus) false string MIXS:0000303 {text} reservoir name -resins_pc resins wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000134 {text};{float} {unit} resins wt% +samp_collec_device sample collection device device name The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method sample collection method PMID,DOI,url , or text The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method samp_collect_point sample collection point enumeration 1 "Sampling 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" well false samp_collect_point_enum MIXS:0001015 sample collection point +samp_dis_stage sample disease stage enumeration 1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. infection false samp_dis_stage_enum MIXS:0000249 sample disease stage +samp_floor sampling floor enumeration 1 The floor of the building, where the sampling room is located 4th floor false samp_floor_enum MIXS:0000828 sampling floor samp_loc_corr_rate corrosion rate at sample location measurement value range millimeter per year 1 Metal 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 false string MIXS:0000136 {float} - {float} {unit} corrosion rate at sample location +samp_mat_process sample material processing text A 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. filtering of seawater, storing samples in ethanol false string MIXS:0000016 {text} sample material processing samp_md sample measured depth measurement value;enumeration meter 1 "In 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" 1534 meter;MSL false string MIXS:0000413 sample measured depth +samp_name sample name text A 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. ISDsoil1 false string MIXS:0001107 {text} sample name samp_preserv preservative added to sample name;measurement value milliliter 1 Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) false string MIXS:0000463 {text};{float} {unit} preservative added to sample +samp_room_id sampling room ID or name value 1 Sampling room number. This ID should be consistent with the designations on the building floor plans false string MIXS:0000244 sampling room ID or name +samp_size amount or size of sample collected measurement value millliter, gram, milligram, liter The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 liter false string MIXS:0000001 amount or size of sample collected +samp_sort_meth sample size sorting method description of method m Method 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. false string MIXS:0000216 {text} sample size sorting method samp_store_dur sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp sample storage temperature measurement value degree Celsius 1 Temperature at which sample was stored, e.g. -80 degree Celsius -80 degree Celsius false string MIXS:0000110 sample storage temperature samp_subtype sample subtype enumeration 1 "Name 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" biofilm false samp_subtype_enum MIXS:0000999 sample subtype +samp_time_out sampling time outside time hour 1 The recent and long term history of outside sampling false string MIXS:0000196 sampling time outside samp_transport_cond sample transport conditions measurement value;measurement value days;degree Celsius 1 Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) 5 days;-20 degree Celsius false string MIXS:0000410 {float} {unit};{float} {unit} sample transport conditions samp_tvdss sample true vertical depth subsea measurement value or measurement value range meter 1 Depth 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 false string MIXS:0000409 {float}-{float} {unit} sample true vertical depth subsea samp_type sample type GENEPIO:0001246 1 The 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). built environment sample [GENEPIO:0001248] false string MIXS:0000998 {termLabel} {[termID]} sample type +samp_weather sampling day weather enumeration 1 The weather on the sampling day foggy false samp_weather_enum MIXS:0000827 sampling day weather samp_well_name sample well name name 1 Name of the well (e.g. BXA1123) where sample was taken false string MIXS:0000296 {text} sample well name +sample_link This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false string true {text}:{text} sample linkage +sample_shipped This field is only required when completing metadata for samples being submitted to EMSL for analyses. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. 15 g|100 uL|5 mL true {float} {unit} sample shipped amount +sample_type This can vary from 'environmental package' if the sample is an extraction. Type of sample being submitted water extracted soil sample_type_enum true sample type saturates_pc saturates wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false string MIXS:0000131 {text};{float} {unit} saturates wt% +season season NCIT:C94729 1 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). autumn [NCIT:C94733] false string MIXS:0000829 {termLabel} {[termID]} season +season_environment seasonal environment seasonal environment name;treatment interval and duration m Treatment 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 rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001068 {text};{Rn/start_time/end_time/duration} seasonal environment +season_precpt mean seasonal precipitation measurement value millimeter 1 The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. false string MIXS:0000645 mean seasonal precipitation +season_temp mean seasonal temperature measurement value degree Celsius 1 Mean seasonal temperature 18 degree Celsius false string MIXS:0000643 mean seasonal temperature +season_use seasonal use enumeration 1 The seasons the space is occupied Winter false season_use_enum MIXS:0000830 seasonal use secondary_treatment secondary treatment secondary treatment type 1 The process for substantially degrading the biological content of the sewage false string MIXS:0000351 {text} secondary treatment +sediment_type sediment type enumeration 1 Information about the sediment type based on major constituents biogenous false sediment_type_enum MIXS:0001078 sediment type sewage_type sewage type sewage type name 1 Type of wastewater treatment plant as municipial or industrial false string MIXS:0000215 {text} sewage type +shad_dev_water_mold shading device signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the shading device no presence of mold visible false string MIXS:0000834 [presence of mold visible|no presence of mold visible] shading device signs of water/mold +shading_device_cond shading device condition enumeration 1 The physical condition of the shading device at the time of sampling new false shading_device_cond_enum MIXS:0000831 shading device condition +shading_device_loc shading device location enumeration 1 The location of the shading device in relation to the built structure exterior false string MIXS:0000832 [exterior|interior] shading device location +shading_device_mat shading device material material name 1 The material the shading device is composed of false string MIXS:0000245 {text} shading device material +shading_device_type shading device type enumeration 1 The type of shading device slatted aluminum awning false shading_device_type_enum MIXS:0000835 shading device type +sieving composite design/sieving design name and/or size;amount 1 Collection design of pooled samples and/or sieve size and amount of sample sieved false string MIXS:0000322 {{text}|{float} {unit}};{float} {unit} composite design/sieving +silicate silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false string MIXS:0000184 silicate +size_frac size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +size_frac_low size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false string MIXS:0000735 size-fraction lower threshold +size_frac_up size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false string MIXS:0000736 size-fraction upper threshold +slope_aspect slope aspect measurement value degree 1 The 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. false string MIXS:0000647 slope aspect +slope_gradient slope gradient measurement value percentage 1 Commonly 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 false string MIXS:0000646 slope gradient sludge_retent_time sludge retention time measurement value hours 1 The time activated sludge remains in reactor false string MIXS:0000669 sludge retention time sodium sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false string MIXS:0000428 sodium +soil_horizon soil horizon enumeration 1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath A horizon false soil_horizon_enum MIXS:0001082 soil horizon +soil_text_measure soil texture measurement measurement value 1 The 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. false string MIXS:0000335 soil texture measurement +soil_texture_meth soil texture method PMID,DOI or url 1 Reference or method used in determining soil texture false string MIXS:0000336 {PMID}|{DOI}|{URL} soil texture method +soil_type soil type ENVO_00001998 1 Description 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. plinthosol [ENVO:00002250] false string MIXS:0000332 {termLabel} {[termID]} soil type +soil_type_meth soil type method PMID,DOI or url 1 Reference or method used in determining soil series name or other lower-level classification false string MIXS:0000334 {PMID}|{DOI}|{URL} soil type method +solar_irradiance solar irradiance measurement value kilowatts per square meter per day, ergs per square centimeter per second 1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval 1.36 kilowatts per square meter per day false string MIXS:0000112 solar irradiance soluble_inorg_mat soluble inorganic material soluble inorganic material name;measurement value gram, microgram, mole per liter, gram per liter, parts per million m Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. false string MIXS:0000672 {text};{float} {unit} soluble inorganic material soluble_org_mat soluble organic material soluble organic material name;measurement value gram, microgram, mole per liter, gram per liter, parts per million m Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. false string MIXS:0000673 {text};{float} {unit} soluble organic material +soluble_react_phosp soluble reactive phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of soluble reactive phosphorus 0.1 milligram per liter false string MIXS:0000738 soluble reactive phosphorus +source_mat_id source material identifiers for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer A 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). MPI012345 false string MIXS:0000026 {text} source material identifiers +space_typ_state space typical state enumeration 1 Customary or normal state of the space typically occupied false string MIXS:0000770 [typically occupied|typically unoccupied] space typical state +specific specifications enumeration 1 The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents construction false specific_enum MIXS:0000836 specifications +specific_ecosystem Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. +specific_humidity specific humidity measurement value gram of air, kilogram of air 1 The 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. 15 per kilogram of air false string MIXS:0000214 specific humidity sr_dep_env source rock depositional environment enumeration 1 "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If ""other"" is specified, please propose entry in ""additional info"" field" Marine false sr_dep_env_enum MIXS:0000996 source rock depositional environment sr_geol_age source rock geological age enumeration 1 "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false sr_geol_age_enum MIXS:0000997 source rock geological age sr_kerog_type source rock kerogen type enumeration 1 "Origin 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" Type IV false sr_kerog_type_enum MIXS:0000994 source rock kerogen type sr_lithology source rock lithology enumeration 1 "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If ""other"" is specified, please propose entry in ""additional info"" field" Coal false sr_lithology_enum MIXS:0000995 source rock lithology +standing_water_regm standing water regimen standing water type;treatment interval and duration m Treatment 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 standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001069 {text};{Rn/start_time/end_time/duration} standing water regimen +start_date_inc Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only true {date, arbitrary precision} incubation start date +start_time_inc Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} incubation start time, GMT +store_cond storage conditions storage condition type;duration 1 Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). -20 degree Celsius freezer;P2Y10D false string MIXS:0000327 {text};{duration} storage conditions +substructure_type substructure type enumeration m The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level basement true substructure_type_enum MIXS:0000767 substructure type +sulfate sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false string MIXS:0000423 sulfate sulfate_fw sulfate in formation water measurement value milligram per liter 1 Original sulfate concentration in the hydrocarbon resource false string MIXS:0000407 sulfate in formation water sulfide sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false string MIXS:0000424 sulfide +surf_air_cont surface-air contaminant enumeration m Contaminant identified on surface radon true surf_air_cont_enum MIXS:0000759 surface-air contaminant +surf_humidity surface humidity measurement value percentage 1 Surfaces: water activity as a function of air and material moisture 10% false string MIXS:0000123 surface humidity +surf_material surface material enumeration 1 Surface materials at the point of sampling wood false surf_material_enum MIXS:0000758 surface material +surf_moisture surface moisture measurement value parts per million, gram per cubic meter, gram per square meter 1 Water held on a surface 0.01 gram per square meter false string MIXS:0000128 surface moisture +surf_moisture_ph surface moisture pH measurement value 1 ph measurement of surface 7 false double MIXS:0000760 surface moisture pH +surf_temp surface temperature measurement value degree Celsius 1 Temperature of the surface at the time of sampling 15 degree Celsius false string MIXS:0000125 surface temperature +suspend_part_matter suspended particulate matter measurement value milligram per liter 1 Concentration of suspended particulate matter 0.5 milligram per liter false string MIXS:0000741 suspended particulate matter suspend_solids suspended solids suspended solid name;measurement value gram, microgram, milligram per liter, mole per liter, gram per liter, part per million m Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances false string MIXS:0000150 {text};{float} {unit} suspended solids tan total acid number measurement value milligram per liter 1 Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) false string MIXS:0000120 total acid number -tertiary_treatment tertiary treatment tertiary treatment type 1 The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment false string MIXS:0000352 {text} tertiary treatment -toluene toluene measurement value milligram per liter, parts per million 1 Concentration of toluene in the sample false string MIXS:0000154 toluene -tot_iron total iron measurement value milligram per liter, milligram per kilogram 1 Concentration of total iron in the sample false string MIXS:0000105 total iron -tot_nitro total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false string MIXS:0000102 total nitrogen concentration -tot_phosphate total phosphate measurement value microgram per liter, micromole per liter 1 Total amount or concentration of phosphate false string MIXS:0000689 total phosphate -tot_sulfur total sulfur measurement value milligram per liter, parts per million 1 Concentration of total sulfur in the sample false string MIXS:0000419 total sulfur -tvdss_of_hcr_press depth (TVDSS) of hydrocarbon resource pressure measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). false string MIXS:0000397 depth (TVDSS) of hydrocarbon resource pressure -tvdss_of_hcr_temp depth (TVDSS) of hydrocarbon resource temperature measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). false string MIXS:0000394 depth (TVDSS) of hydrocarbon resource temperature -vfa volatile fatty acids measurement value milligram per liter, parts per million 1 Concentration of Volatile Fatty Acids in the sample false string MIXS:0000152 volatile fatty acids -vfa_fw vfa in formation water measurement value milligram per liter 1 Original volatile fatty acid concentration in the hydrocarbon resource false string MIXS:0000408 vfa in formation water -viscosity viscosity measurement value;measurement value cP at degree Celsius 1 A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) false string MIXS:0000126 {float} {unit};{float} {unit} viscosity -wastewater_type wastewater type wastewater type name 1 The origin of wastewater such as human waste, rainfall, storm drains, etc. false string MIXS:0000353 {text} wastewater type -water_cut water cut measurement value percent 1 Current amount of water (%) in a produced fluid stream; or the average of the combined streams false string MIXS:0000454 water cut -water_prod_rate water production rate measurement value cubic meter per day 1 Water production rates per well (e.g. 987 m3 / day) false string MIXS:0000453 water production rate -win well identification number text 1 A 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) false string MIXS:0000297 {text} well identification number -xylene xylene measurement value milligram per liter, parts per million 1 Concentration of xylene in the sample false string MIXS:0000156 xylene -collection_time Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} collection time, GMT -collection_date_inc Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was harvested/collected/ended. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only true {date, arbitrary precision} incubation collection date -collection_time_inc Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was harvested/collected/ended. Only relevant for incubation samples. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} incubation collection time, GMT -start_date_inc Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only true {date, arbitrary precision} incubation start date -start_time_inc Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only true {time, seconds optional} incubation start time, GMT -filter_method describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci true {text} filter method -experimental_factor_other This slot accepts open-ended text about your sample.|We recommend using key:value pairs.|Provided pairs will be considered for inclusion as future slots/terms in this data collection template. Other details about your sample that you feel can't be accurately represented in the available columns. experimental treatment: value true {text} experimental factor- other -non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g {text};{float} {unit} non-microbial biomass -non_microb_biomass_method "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 {PMID}|{DOI}|{URL} non-microbial biomass method -microbial_biomass_c If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil {float} {unit} microbial biomass carbon -micro_biomass_c_meth "required if ""microbial_biomass_c"" is provided" Reference or method used in determining microbial biomass carbon https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 true {PMID}|{DOI}|{URL} microbial biomass carbon method How should we separate values? | or ;? lets be consistent -microbial_biomass_n If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil {float} {unit} microbial biomass nitrogen -micro_biomass_n_meth "required if ""microbial_biomass_n"" is provided" Reference or method used in determining microbial biomass nitrogen https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 {PMID}|{DOI}|{URL} microbial biomass nitrogen method -org_nitro_method "required if ""org_nitro"" is provided" Method used for obtaining organic nitrogen https://doi.org/10.1016/0038-0717(85)90144-0 {PMID}|{DOI}|{URL} organic nitrogen method -other_treatment This is an open text field to provide any treatments that cannot be captured in the provided slots. Other treatments applied to your samples that are not applicable to the provided fields true {text} other treatments -isotope_exposure This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? -lbc_thirty lbc_thirty|lbc30|lime buffer capacity (at 30 minutes) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined after 30 minute incubation 543 mg/kg false string lime buffer capacity (at 30 minutes) -lbceq lbceq|lime buffer capacity (at 5-day equilibrium) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined at equilibrium after 5 day incubation 1575 mg/kg false string lime buffer capacity (after 5 day incubation) -manganese manganese measurement value mg/kg (ppm) 1 Concentration of manganese in the sample 24.7 mg/kg false string manganese -zinc zinc measurement value mg/kg (ppm) 1 Concentration of zinc in the sample 2.5 mg/kg false string zinc -ammonium_nitrogen ammonium_nitrogen|NH4-N measurement value mg/kg 1 Concentration of ammonium nitrogen in the sample 2.3 mg/kg false string ammonium nitrogen -nitrate_nitrogen nitrate_nitrogen|NO3-N measurement value mg/kg 1 often below some specified limit of detection Concentration of nitrate nitrogen in the sample 0.29 mg/kg false string nitrate_nitrogen -nitrite_nitrogen nitrite_nitrogen|NO2-N measurement value mg/kg 1 Concentration of nitrite nitrogen in the sample 1.2 mg/kg false string nitrite_nitrogen -growth_facil growth facility free text or CO 1 Type 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 Growth chamber [CO_715:0000189] false string MIXS:0001043 {text}|{termLabel} {[termID]} growth facility -store_cond storage conditions storage condition type;duration 1 Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other). -20 degree Celsius freezer;P2Y10D false string MIXS:0000327 {text};{duration} storage conditions -collection_date collection date date and time The 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 2018-05-11T10:00:00+01:00; 2018-05-11 false string MIXS:0000011 collection date -geo_loc_name geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The 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) USA: Maryland, Bethesda false string MIXS:0000010 {term}: {term}, {text} geographic location (country and/or sea,region) -lat_lon geographic location (latitude and longitude) decimal degrees, limit to 8 decimal points The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system 50.586825 6.408977 false string MIXS:0000009 {float} {float} geographic location (latitude and longitude) -elev elevation measurement value Elevation 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. 100 meter false string MIXS:0000093 elevation -samp_store_temp sample storage temperature measurement value degree Celsius 1 Temperature at which sample was stored, e.g. -80 degree Celsius -80 degree Celsius false string MIXS:0000110 sample storage temperature -sieving composite design/sieving design name and/or size;amount 1 Collection design of pooled samples and/or sieve size and amount of sample sieved false string MIXS:0000322 {{text}|{float} {unit}};{float} {unit} composite design/sieving -depth depth measurement value The 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. 10 meter false string MIXS:0000018 depth -size_frac_low size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false string MIXS:0000735 size-fraction lower threshold -size_frac_up size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false string MIXS:0000736 size-fraction upper threshold -samp_mat_process sample material processing text A 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. filtering of seawater, storing samples in ethanol false string MIXS:0000016 {text} sample material processing -biotic_regm biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string MIXS:0001038 {text} biotic regimen -samp_collec_device sample collection device device name The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method sample collection method PMID,DOI,url , or text The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -air_temp_regm air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen -chem_administration chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11T20:00Z false string MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size amount or size of sample collected measurement value millliter, gram, milligram, liter The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 liter false string MIXS:0000001 amount or size of sample collected -climate_environment climate environment climate name;treatment interval and duration m Treatment 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 tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment -gaseous_environment gaseous environment gaseous compound name;gaseous compound amount;treatment interval and duration micromole per liter m Use 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 nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment -humidity_regm humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen -biotic_relationship observed biotic relationship enumeration Description 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 free living false biotic_relationship_enum MIXS:0000028 observed biotic relationship -rel_to_oxygen relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -light_regm light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false string MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen -watering_regm watering regimen measurement value;treatment interval and duration milliliter, liter m Information 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 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000591 {float} {unit};{Rn/start_time/end_time/duration} watering regimen -alt altitude measurement value Altitude 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 100 meter false string MIXS:0000094 altitude -ph pH measurement value 1 Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 false double MIXS:0001001 pH -slope_aspect slope aspect measurement value degree 1 The 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. false string MIXS:0000647 slope aspect -agrochem_addition history/agrochemical additions agrochemical name;agrochemical amount;timestamp gram, mole per liter, milligram per liter m Addition of fertilizers, pesticides, etc. - amount and time of applications roundup;5 milligram per liter;2018-06-21 false string MIXS:0000639 {text};{float} {unit};{timestamp} history/agrochemical additions -al_sat extreme_unusual_properties/Al saturation measurement value percentage 1 Aluminum saturation (esp. For tropical soils) false string MIXS:0000607 extreme_unusual_properties/Al saturation -al_sat_meth extreme_unusual_properties/Al saturation method PMID,DOI or URL 1 Reference or method used in determining Al saturation false string MIXS:0000324 {PMID}|{DOI}|{URL} extreme_unusual_properties/Al saturation method -annual_precpt mean annual precipitation measurement value millimeter 1 The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. false string MIXS:0000644 mean annual precipitation -annual_temp mean annual temperature measurement value degree Celsius 1 Mean annual temperature 12.5 degree Celsius false string MIXS:0000642 mean annual temperature -crop_rotation history/crop rotation crop rotation status;schedule 1 Whether or not crop is rotated, and if yes, rotation schedule yes;R2/2017-01-01/2018-12-31/P6M false string MIXS:0000318 {boolean};{Rn/start_time/end_time/duration} history/crop rotation -cur_land_use current land use enumeration 1 Present state of sample site conifers false cur_land_use_enum MIXS:0001080 current land use -cur_vegetation current vegetation current vegetation type 1 Vegetation classification from one or more standard classification systems, or agricultural crop false string MIXS:0000312 {text} current vegetation -cur_vegetation_meth current vegetation method PMID,DOI or url 1 Reference or method used in vegetation classification false string MIXS:0000314 {PMID}|{DOI}|{URL} current vegetation method -drainage_class drainage classification enumeration 1 Drainage classification from a standard system such as the USDA system well false drainage_class_enum MIXS:0001085 drainage classification -experimental_factor experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -extreme_event history/extreme events date 1 Unusual physical events that may have affected microbial populations false string MIXS:0000320 history/extreme events -fao_class soil_taxonomic/FAO classification enumeration 1 Soil 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 Luvisols false fao_class_enum MIXS:0001083 soil_taxonomic/FAO classification -fire history/fire date 1 Historical and/or physical evidence of fire false string MIXS:0001086 history/fire -flooding history/flooding date 1 Historical and/or physical evidence of flooding false string MIXS:0000319 history/flooding -heavy_metals extreme_unusual_properties/heavy metals heavy metal name;measurement value unit microgram per gram m Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field. mercury;0.09 micrograms per gram false string MIXS:0000652 {text};{float} {unit} extreme_unusual_properties/heavy metals -heavy_metals_meth extreme_unusual_properties/heavy metals method PMID,DOI or url 1 Reference or method used in determining heavy metals false string MIXS:0000343 {PMID}|{DOI}|{URL} extreme_unusual_properties/heavy metals method -horizon_meth soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} soil horizon method -link_class_info link to classification information PMID,DOI or url 1 Link to digitized soil maps or other soil classification information false string MIXS:0000329 {PMID}|{DOI}|{URL} link to classification information -link_climate_info link to climate information PMID,DOI or url 1 Link to climate resource false string MIXS:0000328 {PMID}|{DOI}|{URL} link to climate information -local_class soil_taxonomic/local classification local classification name 1 Soil classification based on local soil classification system false string MIXS:0000330 {text} soil_taxonomic/local classification -misc_param miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -local_class_meth soil_taxonomic/local classification method PMID,DOI or url 1 Reference or method used in determining the local soil classification false string MIXS:0000331 {PMID}|{DOI}|{URL} soil_taxonomic/local classification method -oxy_stat_samp oxygenation status of sample enumeration 1 Oxygenation status of sample aerobic false rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -prev_land_use_meth history/previous land use method PMID,DOI or url 1 Reference or method used in determining previous land use and dates false string MIXS:0000316 {PMID}|{DOI}|{URL} history/previous land use method -previous_land_use history/previous land use land use name;date 1 Previous land use and dates false string MIXS:0000315 {text};{timestamp} history/previous land use -profile_position profile position enumeration 1 Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas summit false profile_position_enum MIXS:0001084 profile position -season_precpt mean seasonal precipitation measurement value millimeter 1 The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. false string MIXS:0000645 mean seasonal precipitation -season_temp mean seasonal temperature measurement value degree Celsius 1 Mean seasonal temperature 18 degree Celsius false string MIXS:0000643 mean seasonal temperature -slope_gradient slope gradient measurement value percentage 1 Commonly 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 false string MIXS:0000646 slope gradient -soil_horizon soil horizon enumeration 1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath A horizon false soil_horizon_enum MIXS:0001082 soil horizon -soil_text_measure soil texture measurement measurement value 1 The 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. false string MIXS:0000335 soil texture measurement -soil_texture_meth soil texture method PMID,DOI or url 1 Reference or method used in determining soil texture false string MIXS:0000336 {PMID}|{DOI}|{URL} soil texture method -soil_type soil type ENVO_00001998 1 Description 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. plinthosol [ENVO:00002250] false string MIXS:0000332 {termLabel} {[termID]} soil type -soil_type_meth soil type method PMID,DOI or url 1 Reference or method used in determining soil series name or other lower-level classification false string MIXS:0000334 {PMID}|{DOI}|{URL} soil type method +technical_reps This field is only required when completing metadata for samples being submitted to EMSL for analyses. If sending technical replicates of the same sample, indicate the replicate count. 2 true {integer} number technical replicate temp temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false string MIXS:0000113 temperature +temp_out temperature outside house measurement value degree Celsius 1 The recorded temperature value at sampling time outside 5 degree Celsius false string MIXS:0000197 temperature outside house +tertiary_treatment tertiary treatment tertiary treatment type 1 The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment false string MIXS:0000352 {text} tertiary treatment +tidal_stage tidal stage enumeration 1 Stage of tide high tide false tidal_stage_enum MIXS:0000750 tidal stage tillage history/tillage enumeration m Note method(s) used for tilling chisel true tillage_enum MIXS:0001081 history/tillage -water_content water content measurement value gram per gram or cubic centimeter per cubic centimeter 1 Water content measurement false string MIXS:0000185 water content -water_cont_soil_meth water content method PMID,DOI or url 1 Reference or method used in determining the water content of soil false string MIXS:0000323 {PMID}|{DOI}|{URL} water content method -ph_meth pH method PMID,DOI or url 1 Reference or method used in determining ph false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -microbial_biomass microbial biomass measurement value ton, kilogram, gram per kilogram soil 1 The 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 false string MIXS:0000650 microbial biomass -micro_biomass_meth microbial biomass method PMID,DOI or url 1 Reference or method used in determining microbial biomass false string MIXS:0000339 {PMID}|{DOI}|{URL} microbial biomass method -carb_nitro_ratio carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false string MIXS:0000310 carbon/nitrogen ratio -org_matter organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false string MIXS:0000204 organic matter -org_nitro organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false string MIXS:0000205 organic nitrogen +tiss_cult_growth_med tissue culture growth media PMID,DOI,url or free text 1 Description of plant tissue culture growth media used https://link.springer.com/content/pdf/10.1007/BF02796489.pdf false string MIXS:0001070 {PMID}|{DOI}|{URL}|{text} tissue culture growth media +toluene toluene measurement value milligram per liter, parts per million 1 Concentration of toluene in the sample false string MIXS:0000154 toluene tot_carb total carbon measurement value microgram per liter 1 Total carbon content false string MIXS:0000525 total carbon -tot_nitro_content total nitrogen content measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen content of the sample false string MIXS:0000530 total nitrogen content +tot_depth_water_col total depth of water column measurement value meter 1 Measurement of total depth of water column 500 meter false string MIXS:0000634 total depth of water column +tot_diss_nitro total dissolved nitrogen measurement value microgram per liter 1 Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen 40 microgram per liter false string MIXS:0000744 total dissolved nitrogen +tot_inorg_nitro total inorganic nitrogen measurement value microgram per liter 1 Total inorganic nitrogen content 40 microgram per liter false string MIXS:0000745 total inorganic nitrogen +tot_iron total iron measurement value milligram per liter, milligram per kilogram 1 Concentration of total iron in the sample false string MIXS:0000105 total iron +tot_nitro total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false string MIXS:0000102 total nitrogen concentration tot_nitro_cont_meth total nitrogen content method PMID,DOI or url 1 Reference or method used in determining the total nitrogen false string MIXS:0000338 {PMID}|{DOI}|{URL} total nitrogen content method -tot_org_carb total organic carbon measurement value gram Carbon per kilogram sample material 1 Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content false string MIXS:0000533 total organic carbon +tot_nitro_content total nitrogen content measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen content of the sample false string MIXS:0000530 total nitrogen content tot_org_c_meth total organic carbon method PMID,DOI or url 1 Reference or method used in determining total organic carbon false string MIXS:0000337 {PMID}|{DOI}|{URL} total organic carbon method +tot_org_carb total organic carbon measurement value gram Carbon per kilogram sample material 1 Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content false string MIXS:0000533 total organic carbon +tot_part_carb total particulate carbon measurement value microgram per liter, micromole per liter 1 Total particulate carbon content 35 micromole per liter false string MIXS:0000747 total particulate carbon tot_phosp total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false string MIXS:0000117 total phosphorus -phosphate phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false string MIXS:0000505 phosphate -salinity salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false string MIXS:0000183 salinity -salinity_meth salinity method PMID,DOI or url 1 Reference or method used in determining salinity false string MIXS:0000341 {PMID}|{DOI}|{URL} salinity method -samp_name sample name text A 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. ISDsoil1 false string MIXS:0001107 {text} sample name -source_mat_id source material identifiers for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer A 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). MPI012345 false string MIXS:0000026 {text} source material identifiers -analysis_type Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package environmental package MIxS 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 mixs extension false string -sample_link This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false string true {text}:{text} sample linkage -env_broad_scale broad-scale environmental context The major environment type(s) where the sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes. Report 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’s 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 oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean false string MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale local environmental context Environmental entities having causal influences upon the entity at time of sampling. Report the entity or entities which are in the sample or specimen’s 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. litter layer [ENVO:01000338]; Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. false string MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium environmental medium The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483]. Report 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). soil [ENVO:00001998]; Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air [ENVO_00002005] false string MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. -ecosystem_category The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. -ecosystem_type The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. -ecosystem_subtype Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. -specific_ecosystem Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. +tot_phosphate total phosphate measurement value microgram per liter, micromole per liter 1 Total amount or concentration of phosphate false string MIXS:0000689 total phosphate +tot_sulfur total sulfur measurement value milligram per liter, parts per million 1 Concentration of total sulfur in the sample false string MIXS:0000419 total sulfur +train_line train line enumeration 1 The subway line name red false train_line_enum MIXS:0000837 train line +train_stat_loc train station collection location enumeration 1 The train station collection location forest hills false train_stat_loc_enum MIXS:0000838 train station collection location +train_stop_loc train stop collection location enumeration 1 The train stop collection location end false train_stop_loc_enum MIXS:0000839 train stop collection location +turbidity turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false string MIXS:0000191 turbidity +tvdss_of_hcr_press depth (TVDSS) of hydrocarbon resource pressure measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). false string MIXS:0000397 depth (TVDSS) of hydrocarbon resource pressure +tvdss_of_hcr_temp depth (TVDSS) of hydrocarbon resource temperature measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). false string MIXS:0000394 depth (TVDSS) of hydrocarbon resource temperature +typ_occup_density typical occupant density measurement value 1 Customary or normal density of occupants 25 false double MIXS:0000771 typical occupant density +ventilation_rate ventilation rate measurement value cubic meter per minute, liters per second 1 Ventilation rate of the system in the sampled premises 750 cubic meter per minute false string MIXS:0000114 ventilation rate +ventilation_type ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type +vfa volatile fatty acids measurement value milligram per liter, parts per million 1 Concentration of Volatile Fatty Acids in the sample false string MIXS:0000152 volatile fatty acids +vfa_fw vfa in formation water measurement value milligram per liter 1 Original volatile fatty acid concentration in the hydrocarbon resource false string MIXS:0000408 vfa in formation water +vis_media visual media enumeration 1 The building visual media 3D scans false vis_media_enum MIXS:0000840 visual media +viscosity viscosity measurement value;measurement value cP at degree Celsius 1 A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) false string MIXS:0000126 {float} {unit};{float} {unit} viscosity +volatile_org_comp volatile organic compounds volatile organic compound name;measurement value microgram per cubic meter, parts per million, nanogram per liter m Concentration 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 formaldehyde;500 nanogram per liter false string MIXS:0000115 {text};{float} {unit} volatile organic compounds +wall_area wall area measurement value square meter 1 The total area of the sampled room's walls false string MIXS:0000198 wall area +wall_const_type wall construction type enumeration 1 The building class of the wall defined by the composition of the building elements and fire-resistance rating. fire resistive false wall_const_type_enum MIXS:0000841 wall construction type +wall_finish_mat wall finish material enumeration 1 The material utilized to finish the outer most layer of the wall wood false wall_finish_mat_enum MIXS:0000842 wall finish material +wall_height wall height value centimeter 1 The average height of the walls in the sampled room false string MIXS:0000221 wall height +wall_loc wall location enumeration 1 The relative location of the wall within the room north false wall_loc_enum MIXS:0000843 wall location +wall_surf_treatment wall surface treatment enumeration 1 The surface treatment of interior wall paneling false wall_surf_treatment_enum MIXS:0000845 wall surface treatment +wall_texture wall texture enumeration 1 The feel, appearance, or consistency of a wall surface popcorn false wall_texture_enum MIXS:0000846 wall texture +wall_thermal_mass wall thermal mass measurement value joule per degree Celsius 1 The 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 false string MIXS:0000222 wall thermal mass +wall_water_mold wall signs of water/mold enumeration 1 Signs of the presence of mold or mildew on a wall no presence of mold visible false string MIXS:0000844 [presence of mold visible|no presence of mold visible] wall signs of water/mold +wastewater_type wastewater type wastewater type name 1 The origin of wastewater such as human waste, rainfall, storm drains, etc. false string MIXS:0000353 {text} wastewater type +water_cont_soil_meth water content method PMID,DOI or url 1 Reference or method used in determining the water content of soil false string MIXS:0000323 {PMID}|{DOI}|{URL} water content method +water_content water content measurement value gram per gram or cubic centimeter per cubic centimeter 1 Water content measurement false string MIXS:0000185 water content +water_current water current measurement value cubic meter per second, knots 1 Measurement of magnitude and direction of flow within a fluid 10 cubic meter per second false string MIXS:0000203 water current +water_cut water cut measurement value percent 1 Current amount of water (%) in a produced fluid stream; or the average of the combined streams false string MIXS:0000454 water cut +water_feat_size water feature size measurement value square meter 1 The size of the water feature false string MIXS:0000223 water feature size +water_feat_type water feature type enumeration 1 The type of water feature present within the building being sampled stream false water_feat_type_enum MIXS:0000847 water feature type +water_prod_rate water production rate measurement value cubic meter per day 1 Water production rates per well (e.g. 987 m3 / day) false string MIXS:0000453 water production rate +water_temp_regm water temperature regimen measurement value;treatment interval and duration degree Celsius m Information 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 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000590 {float} {unit};{Rn/start_time/end_time/duration} water temperature regimen +watering_regm watering regimen measurement value;treatment interval and duration milliliter, liter m Information 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 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000591 {float} {unit};{Rn/start_time/end_time/duration} watering regimen +weekday weekday enumeration 1 The day of the week when sampling occurred Sunday false weekday_enum MIXS:0000848 weekday +win well identification number text 1 A 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) false string MIXS:0000297 {text} well identification number +wind_direction wind direction wind direction name 1 Wind direction is the direction from which a wind originates Northwest false string MIXS:0000757 {text} wind direction +wind_speed wind speed measurement value meter per second, kilometer per hour 1 Speed of wind measured at the time of sampling 21 kilometer per hour false string MIXS:0000118 wind speed +window_cond window condition enumeration 1 The physical condition of the window at the time of sampling rupture false window_cond_enum MIXS:0000849 window condition +window_cover window covering enumeration 1 The type of window covering curtains false window_cover_enum MIXS:0000850 window covering +window_horiz_pos window horizontal position enumeration 1 The horizontal position of the window on the wall middle false window_horiz_pos_enum MIXS:0000851 window horizontal position +window_loc window location enumeration 1 The relative location of the window within the room west false window_loc_enum MIXS:0000852 window location +window_mat window material enumeration 1 The type of material used to finish a window wood false window_mat_enum MIXS:0000853 window material +window_open_freq window open frequency value 1 The number of times windows are opened per week false string MIXS:0000246 window open frequency +window_size window area/size measurement value inch, meter 1 The window's length and width false string MIXS:0000224 {float} {unit} x {float} {unit} window area/size +window_status window status enumeration 1 Defines whether the windows were open or closed during environmental testing open false string MIXS:0000855 [closed|open] window status +window_type window type enumeration 1 The type of windows fixed window false window_type_enum MIXS:0000856 window type +window_vert_pos window vertical position enumeration 1 The vertical position of the window on the wall middle false window_vert_pos_enum MIXS:0000857 window vertical position +window_water_mold window signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the window. no presence of mold visible false string MIXS:0000854 [presence of mold visible|no presence of mold visible] window signs of water/mold +xylene xylene measurement value milligram per liter, parts per million 1 Concentration of xylene in the sample false string MIXS:0000156 xylene +zinc zinc measurement value mg/kg (ppm) 1 Concentration of zinc in the sample 2.5 mg/kg false string zinc +core field basic fields +alternative_identifiers A list of alternative identifiers for the entity. false string +description a human-readable description of a thing false string dcterms:description name A human readable label for an entity false string +investigation field field describing aspect of the investigation/study to which the sample belongs id A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI nmdc:mgmag-00-x012.1_7_c1 true abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?|a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters will be accepted|typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked via per-class id slot usage assertions|minting authority shoulders should probably be enumerated and checked in the pattern -language "Should use ISO 639-1 code e.g. ""en"", ""fr""" language code attribute field|property|template field|key|characteristic A attribute of a biosample. Examples: depth, habitat, material. For NMDC, attributes SHOULD be mapped to terms within a MIxS template +language "Should use ISO 639-1 code e.g. ""en"", ""fr""" language code nucleic acid sequence source field gold_path_field This is a grouping for any of the gold path fields false string environment field field describing environmental aspect of a sample -alternative_identifiers A list of alternative identifiers for the entity. false string -description a human-readable description of a thing false string dcterms:description -core field basic fields -investigation field field describing aspect of the investigation/study to which the sample belongs AirInterface air dh_interface Air -methane AirInterface methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000101 methane -organism_count AirInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -perturbation AirInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation -samp_store_loc AirInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location air_PM_concen AirInterface air particulate matter concentration particulate matter name;measurement value micrograms per cubic meter m Concentration 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 PM2.5;10 microgram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000108 {text};{float} {unit} air particulate matter concentration +alt AirInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +analysis_type AirInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type barometric_press AirInterface barometric pressure measurement value millibar 1 Force per unit area exerted against a surface by the weight of air above that surface 5 millibar false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000096 barometric pressure carb_dioxide AirInterface carbon dioxide measurement value micromole per liter, parts per million 1 Carbon dioxide (gas) amount or concentration at the time of sampling 410 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000097 carbon dioxide carb_monoxide AirInterface carbon monoxide measurement value micromole per liter, parts per million 1 Carbon monoxide (gas) amount or concentration at the time of sampling 0.1 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000098 carbon monoxide -humidity AirInterface humidity measurement value gram per cubic meter 1 Amount of water vapour in the air, at the time of sampling 25 gram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000100 humidity -oxygen AirInterface oxygen measurement value milligram per liter, parts per million 1 Oxygen (gas) amount or concentration at the time of sampling 600 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000104 oxygen -pollutants AirInterface pollutants pollutant name;measurement value gram, mole per liter, milligram per liter, microgram per cubic meter m Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant lead;0.15 microgram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000107 {text};{float} {unit} pollutants -solar_irradiance AirInterface solar irradiance measurement value kilowatts per square meter per day, ergs per square centimeter per second 1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval 1.36 kilowatts per square meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000112 solar irradiance -ventilation_rate AirInterface ventilation rate measurement value cubic meter per minute, liters per second 1 Ventilation rate of the system in the sampled premises 750 cubic meter per minute false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000114 ventilation rate -ventilation_type AirInterface ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type -volatile_org_comp AirInterface volatile organic compounds volatile organic compound name;measurement value microgram per cubic meter, parts per million, nanogram per liter m Concentration 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 formaldehyde;500 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000115 {text};{float} {unit} volatile organic compounds -wind_direction AirInterface wind direction wind direction name 1 Wind direction is the direction from which a wind originates Northwest false string MIXS:0000757 {text} wind direction -wind_speed AirInterface wind speed measurement value meter per second, kilometer per hour 1 Speed of wind measured at the time of sampling 21 kilometer per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000118 wind speed -size_frac AirInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -samp_store_dur AirInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +chem_administration AirInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration collection_date AirInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name AirInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon AirInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev AirInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp AirInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature depth AirInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process AirInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device AirInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method AirInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration AirInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size AirInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen AirInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt AirInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +ecosystem AirInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category AirInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype AirInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type AirInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev AirInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale AirInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale AirInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium AirInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package AirInterface environmental package MIxS 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 mixs extension false string experimental_factor AirInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +geo_loc_name AirInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) horizon_meth AirInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +humidity AirInterface humidity measurement value gram per cubic meter 1 Amount of water vapour in the air, at the time of sampling 25 gram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000100 humidity +lat_lon AirInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) +methane AirInterface methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000101 methane misc_param AirInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +organism_count AirInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count oxy_stat_samp AirInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp AirInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature +oxygen AirInterface oxygen measurement value milligram per liter, parts per million 1 Oxygen (gas) amount or concentration at the time of sampling 600 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000104 oxygen +perturbation AirInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation +pollutants AirInterface pollutants pollutant name;measurement value gram, mole per liter, milligram per liter, microgram per cubic meter m Pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant lead;0.15 microgram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000107 {text};{float} {unit} pollutants +rel_to_oxygen AirInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen salinity AirInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type AirInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package AirInterface environmental package MIxS 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 mixs extension false string +samp_collec_device AirInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method AirInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process AirInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size AirInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur AirInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc AirInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp AirInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature sample_link AirInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale AirInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale AirInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium AirInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem AirInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category AirInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type AirInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype AirInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +size_frac AirInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +solar_irradiance AirInterface solar irradiance measurement value kilowatts per square meter per day, ergs per square centimeter per second 1 The amount of solar energy that arrives at a specific area of a surface during a specific time interval 1.36 kilowatts per square meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000112 solar irradiance specific_ecosystem AirInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +temp AirInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature +ventilation_rate AirInterface ventilation rate measurement value cubic meter per minute, liters per second 1 Ventilation rate of the system in the sampled premises 750 cubic meter per minute false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000114 ventilation rate +ventilation_type AirInterface ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type +volatile_org_comp AirInterface volatile organic compounds volatile organic compound name;measurement value microgram per cubic meter, parts per million, nanogram per liter m Concentration 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 formaldehyde;500 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000115 {text};{float} {unit} volatile organic compounds +wind_direction AirInterface wind direction wind direction name 1 Wind direction is the direction from which a wind originates Northwest false string MIXS:0000757 {text} wind direction +wind_speed AirInterface wind speed measurement value meter per second, kilometer per hour 1 Speed of wind measured at the time of sampling 21 kilometer per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000118 wind speed BiofilmInterface biofilm dh_interface Biofilm alkalinity BiofilmInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity alkyl_diethers BiofilmInterface alkyl diethers measurement value mole per liter 1 Concentration of alkyl diethers 0.005 mole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000490 alkyl diethers +alt BiofilmInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude aminopept_act BiofilmInterface aminopeptidase activity measurement value mole per liter per hour 1 Measurement of aminopeptidase activity 0.269 mole per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000172 aminopeptidase activity ammonium BiofilmInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type BiofilmInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type bacteria_carb_prod BiofilmInterface bacterial carbon production measurement value nanogram per hour 1 Measurement of bacterial carbon production 2.53 microgram per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000173 bacterial carbon production biomass BiofilmInterface biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000174 {text};{float} {unit} biomass bishomohopanol BiofilmInterface bishomohopanol measurement value microgram per liter, microgram per gram 1 Concentration of bishomohopanol 14 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000175 bishomohopanol bromide BiofilmInterface bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000176 bromide calcium BiofilmInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +carb_nitro_ratio BiofilmInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio +chem_administration BiofilmInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chloride BiofilmInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride chlorophyll BiofilmInterface chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000177 chlorophyll +collection_date BiofilmInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +depth BiofilmInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters diether_lipids BiofilmInterface diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000178 {text};{float} {unit} diether lipids diss_carb_dioxide BiofilmInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide diss_hydrogen BiofilmInterface dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000179 dissolved hydrogen @@ -658,83 +660,76 @@ diss_inorg_carb BiofilmInterface dissolved inorganic carbon measurement value m diss_org_carb BiofilmInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon diss_org_nitro BiofilmInterface dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000162 dissolved organic nitrogen diss_oxygen BiofilmInterface dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000119 dissolved oxygen +ecosystem BiofilmInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category BiofilmInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype BiofilmInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type BiofilmInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev BiofilmInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale BiofilmInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale BiofilmInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium BiofilmInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package BiofilmInterface environmental package MIxS 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 mixs extension false string +experimental_factor BiofilmInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +geo_loc_name BiofilmInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) glucosidase_act BiofilmInterface glucosidase activity measurement value mol per liter per hour 1 Measurement of glucosidase activity 5 mol per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000137 glucosidase activity +horizon_meth BiofilmInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +lat_lon BiofilmInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) magnesium BiofilmInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium mean_frict_vel BiofilmInterface mean friction velocity measurement value meter per second 1 Measurement of mean friction velocity 0.5 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000498 mean friction velocity mean_peak_frict_vel BiofilmInterface mean peak friction velocity measurement value meter per second 1 Measurement of mean peak friction velocity 1 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000502 mean peak friction velocity methane BiofilmInterface methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000101 methane +misc_param BiofilmInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter n_alkanes BiofilmInterface n-alkanes n-alkane name;measurement value micromole per liter m Concentration of n-alkanes; can include multiple n-alkanes n-hexadecane;100 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000503 {text};{float} {unit} n-alkanes nitrate BiofilmInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate nitrite BiofilmInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite nitro BiofilmInterface nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000504 nitrogen org_carb BiofilmInterface organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000508 organic carbon +org_matter BiofilmInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter +org_nitro BiofilmInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen organism_count BiofilmInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp BiofilmInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample part_org_carb BiofilmInterface particulate organic carbon measurement value microgram per liter 1 Concentration of particulate organic carbon 1.92 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000515 particulate organic carbon perturbation BiofilmInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation petroleum_hydrocarb BiofilmInterface petroleum hydrocarbon measurement value micromole per liter 1 Concentration of petroleum hydrocarbon 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000516 petroleum hydrocarbon +ph BiofilmInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth BiofilmInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method phaeopigments BiofilmInterface phaeopigments phaeopigment name;measurement value milligram per cubic meter m Concentration of phaeopigments; can include multiple phaeopigments 2.5 milligram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000180 {text};{float} {unit} phaeopigments +phosphate BiofilmInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate phosplipid_fatt_acid BiofilmInterface phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid potassium BiofilmInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pressure BiofilmInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure redox_potential BiofilmInterface redox potential measurement value millivolt 1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential 300 millivolt false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000182 redox potential +rel_to_oxygen BiofilmInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity BiofilmInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device BiofilmInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method BiofilmInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process BiofilmInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size BiofilmInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur BiofilmInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration samp_store_loc BiofilmInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp BiofilmInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link BiofilmInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage silicate BiofilmInterface silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000184 silicate -sulfate BiofilmInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate -turbidity BiofilmInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity size_frac BiofilmInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -samp_store_dur BiofilmInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration sodium BiofilmInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium +specific_ecosystem BiofilmInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +sulfate BiofilmInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate sulfide BiofilmInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide -collection_date BiofilmInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name BiofilmInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon BiofilmInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev BiofilmInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp BiofilmInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth BiofilmInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process BiofilmInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device BiofilmInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method BiofilmInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration BiofilmInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size BiofilmInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen BiofilmInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt BiofilmInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph BiofilmInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor BiofilmInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth BiofilmInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param BiofilmInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp BiofilmInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample temp BiofilmInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -water_content BiofilmInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? -ph_meth BiofilmInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -carb_nitro_ratio BiofilmInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio -org_matter BiofilmInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter -org_nitro BiofilmInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen tot_carb BiofilmInterface Total carbon content 1 ug/L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000525 total carbon is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format|is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format tot_nitro_content BiofilmInterface Total nitrogen content of the sample 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000530 total nitrogen content tot_org_carb BiofilmInterface Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000533 total organic carbon check description. How are they different?|check description. How are they different? -phosphate BiofilmInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity BiofilmInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type BiofilmInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package BiofilmInterface environmental package MIxS 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 mixs extension false string -sample_link BiofilmInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale BiofilmInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale BiofilmInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium BiofilmInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem BiofilmInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category BiofilmInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type BiofilmInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype BiofilmInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem BiofilmInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +turbidity BiofilmInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity +water_content BiofilmInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? BuiltEnvInterface built_env dh_interface Built Env -organism_count BuiltEnvInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -carb_dioxide BuiltEnvInterface carbon dioxide measurement value micromole per liter, parts per million 1 Carbon dioxide (gas) amount or concentration at the time of sampling 410 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000097 carbon dioxide -ventilation_type BuiltEnvInterface ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type abs_air_humidity BuiltEnvInterface absolute air humidity measurement value gram per gram, kilogram per kilogram, kilogram, pound 1 Actual mass of water vapor - mh20 - present in the air water vapor mixture 9 gram per gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000122 absolute air humidity address BuiltEnvInterface address value 1 The street name and building number where the sampling occurred. false string MIXS:0000218 {integer}{text} address adj_room BuiltEnvInterface adjacent rooms room name;room number 1 List of rooms (room number, room name) immediately adjacent to the sampling room false string MIXS:0000219 {text};{integer} adjacent rooms aero_struc BuiltEnvInterface aerospace structure enumeration 1 Aerospace 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 plane false string MIXS:0000773 [plane|glider] aerospace structure air_temp BuiltEnvInterface air temperature measurement value degree Celsius 1 Temperature of the air at the time of sampling 20 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000124 air temperature +alt BuiltEnvInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude amount_light BuiltEnvInterface amount of light measurement value lux, lumens per square meter 1 The unit of illuminance and luminous emittance, measuring luminous flux per unit area false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000140 amount of light +analysis_type BuiltEnvInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type arch_struc BuiltEnvInterface architectural structure enumeration 1 An architectural structure is a human-made, free-standing, immobile outdoor construction shed false arch_struc_enum MIXS:0000774 architectural structure avg_dew_point BuiltEnvInterface average dew point measurement value degree Celsius 1 The average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day 25.5 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000141 average dew point avg_occup BuiltEnvInterface average daily occupancy value 1 Daily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room. 2 false string MIXS:0000775 average daily occupancy @@ -747,6 +742,7 @@ building_setting BuiltEnvInterface building setting enumeration 1 A location built_struc_age BuiltEnvInterface built structure age value year 1 The age of the built structure since construction 15 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000145 built structure age built_struc_set BuiltEnvInterface built structure setting enumeration 1 The characterization of the location of the built structure as high or low human density rural false string MIXS:0000778 [urban|rural] built structure setting built_struc_type BuiltEnvInterface built structure type free text 1 A physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads false string MIXS:0000721 {text} built structure type +carb_dioxide BuiltEnvInterface carbon dioxide measurement value micromole per liter, parts per million 1 Carbon dioxide (gas) amount or concentration at the time of sampling 410 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000097 carbon dioxide ceil_area BuiltEnvInterface ceiling area measurement value square meter 1 The area of the ceiling space within the room 25 square meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000148 ceiling area ceil_cond BuiltEnvInterface ceiling condition enumeration 1 The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas damaged false ceil_cond_enum MIXS:0000779 ceiling condition ceil_finish_mat BuiltEnvInterface ceiling finish material enumeration 1 The type of material used to finish a ceiling stucco false ceil_finish_mat_enum MIXS:0000780 ceiling finish material @@ -755,8 +751,10 @@ ceil_texture BuiltEnvInterface ceiling texture enumeration 1 The feel, appear ceil_thermal_mass BuiltEnvInterface ceiling thermal mass measurement value joule per degree Celsius 1 The 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 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000143 ceiling thermal mass ceil_type BuiltEnvInterface ceiling type enumeration 1 The type of ceiling according to the ceiling's appearance or construction coffered false ceil_type_enum MIXS:0000784 ceiling type ceil_water_mold BuiltEnvInterface ceiling signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the ceiling presence of mold visible false string MIXS:0000781 [presence of mold visible|no presence of mold visible] ceiling signs of water/mold +collection_date BuiltEnvInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date cool_syst_id BuiltEnvInterface cooling system identifier unique identifier 1 The cooling system identifier 12345 false string MIXS:0000785 cooling system identifier date_last_rain BuiltEnvInterface date last rain timestamp 1 The date of the last time it rained 2018-05-11:T14:30Z false string MIXS:0000786 date last rain +depth BuiltEnvInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters dew_point BuiltEnvInterface dew point measurement value degree Celsius 1 The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water. 22 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000129 dew point door_comp_type BuiltEnvInterface door type, composite enumeration 1 The composite type of the door revolving false door_comp_type_enum MIXS:0000795 door type, composite door_cond BuiltEnvInterface door condition enumeration 1 The phsical condition of the door new false door_cond_enum MIXS:0000788 door condition @@ -770,10 +768,20 @@ door_type_metal BuiltEnvInterface door type, metal enumeration 1 The type of door_type_wood BuiltEnvInterface door type, wood enumeration 1 The type of wood door battened false door_type_wood_enum MIXS:0000797 door type, wood door_water_mold BuiltEnvInterface door signs of water/mold enumeration 1 Signs of the presence of mold or mildew on a door presence of mold visible false string MIXS:0000793 [presence of mold visible|no presence of mold visible] door signs of water/mold drawings BuiltEnvInterface drawings enumeration 1 The buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents sketch false drawings_enum MIXS:0000798 drawings +ecosystem BuiltEnvInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category BuiltEnvInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype BuiltEnvInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type BuiltEnvInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev BuiltEnvInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters elevator BuiltEnvInterface elevator count value 1 The number of elevators within the built structure 2 false string MIXS:0000799 elevator count +env_broad_scale BuiltEnvInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale BuiltEnvInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium BuiltEnvInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package BuiltEnvInterface environmental package MIxS 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 mixs extension false string escalator BuiltEnvInterface escalator count value 1 The number of escalators within the built structure 4 false string MIXS:0000800 escalator count exp_duct BuiltEnvInterface exposed ductwork measurement value square meter 1 The amount of exposed ductwork in the room false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000144 exposed ductwork exp_pipe BuiltEnvInterface exposed pipes measurement value 1 The number of exposed pipes in the room false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000220 exposed pipes +experimental_factor BuiltEnvInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor ext_door BuiltEnvInterface exterior door count value 1 The number of exterior doors in the built structure false string MIXS:0000170 exterior door count ext_wall_orient BuiltEnvInterface orientations of exterior wall enumeration 1 The orientation of the exterior wall northwest false ext_wall_orient_enum MIXS:0000817 orientations of exterior wall ext_window_orient BuiltEnvInterface orientations of exterior window enumeration 1 The compass direction the exterior window of the room is facing southwest false ext_window_orient_enum MIXS:0000818 orientations of exterior window @@ -791,6 +799,7 @@ freq_clean BuiltEnvInterface frequency of cleaning enumeration or {text} 1 Th freq_cook BuiltEnvInterface frequency of cooking measurement value 1 The number of times a meal is cooked per week false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000227 frequency of cooking furniture BuiltEnvInterface furniture enumeration 1 The types of furniture present in the sampled room chair false furniture_enum MIXS:0000807 furniture gender_restroom BuiltEnvInterface gender of restroom enumeration 1 The gender type of the restroom male false gender_restroom_enum MIXS:0000808 gender of restroom +geo_loc_name BuiltEnvInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) hall_count BuiltEnvInterface hallway/corridor count value 1 The total count of hallways and cooridors in the built structure false string MIXS:0000228 hallway/corridor count handidness BuiltEnvInterface handidness enumeration 1 The handidness of the individual sampled right handedness false handidness_enum MIXS:0000809 handidness heat_cool_type BuiltEnvInterface heating and cooling system type enumeration m Methods of conditioning or heating a room or building heat pump true heat_cool_type_enum MIXS:0000766 heating and cooling system type @@ -798,11 +807,13 @@ heat_deliv_loc BuiltEnvInterface heating delivery locations enumeration 1 The heat_sys_deliv_meth BuiltEnvInterface heating system delivery method enumeration 1 The method by which the heat is delivered through the system radiant false string MIXS:0000812 [conductive|radiant] heating system delivery method heat_system_id BuiltEnvInterface heating system identifier unique identifier 1 The heating system identifier false string MIXS:0000833 heating system identifier height_carper_fiber BuiltEnvInterface height carpet fiber mat value centimeter 1 The average carpet fiber height in the indoor environment false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000167 height carpet fiber mat +horizon_meth BuiltEnvInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method indoor_space BuiltEnvInterface indoor space enumeration 1 A distinguishable space within a structure, the purpose for which discrete areas of a building is used foyer false indoor_space_enum MIXS:0000763 indoor space indoor_surf BuiltEnvInterface indoor surface enumeration 1 Type of indoor surface wall false indoor_surf_enum MIXS:0000764 indoor surface inside_lux BuiltEnvInterface inside lux light measurement value kilowatt per square metre 1 The recorded value at sampling time (power density) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000168 inside lux light int_wall_cond BuiltEnvInterface interior wall condition enumeration 1 The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas damaged false int_wall_cond_enum MIXS:0000813 interior wall condition last_clean BuiltEnvInterface last time swept/mopped/vacuumed timestamp 1 The last time the floor was cleaned (swept, mopped, vacuumed) 2018-05-11:T14:30Z false string MIXS:0000814 last time swept/mopped/vacuumed +lat_lon BuiltEnvInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) light_type BuiltEnvInterface light type enumeration m Application 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 desk lamp true light_type_enum MIXS:0000769 light type max_occup BuiltEnvInterface maximum occupancy measurement value 1 The maximum amount of people allowed in the indoor environment false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000229 maximum occupancy mech_struc BuiltEnvInterface mechanical structure enumeration 1 mechanical structure: a moving structure elevator false mech_struc_enum MIXS:0000815 mechanical structure @@ -812,6 +823,7 @@ number_resident BuiltEnvInterface number of residents measurement value 1 The occup_density_samp BuiltEnvInterface occupant density at sampling measurement value 1 Average number of occupants at time of sampling per square footage false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000217 occupant density at sampling occup_document BuiltEnvInterface occupancy documentation enumeration 1 The type of documentation of occupancy estimate false occup_document_enum MIXS:0000816 occupancy documentation occup_samp BuiltEnvInterface occupancy at sampling measurement value 1 Number of occupants present at time of sample within the given space 10 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000772 occupancy at sampling +organism_count BuiltEnvInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count pres_animal_insect BuiltEnvInterface presence of pets, animals, or insects enumeration;count 1 The type and number of animals or insects present in the sampling space. cat;5 false ^(cat|dog|rodent|snake|other);\d+$ string MIXS:0000819 presence of pets, animals, or insects quad_pos BuiltEnvInterface quadrant position enumeration 1 The quadrant position of the sampling room within the building West side false quad_pos_enum MIXS:0000820 quadrant position rel_air_humidity BuiltEnvInterface relative air humidity measurement value percentage 1 Partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air 80% false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000121 relative air humidity @@ -840,6 +852,7 @@ samp_room_id BuiltEnvInterface sampling room ID or name value 1 Sampling room samp_sort_meth BuiltEnvInterface sample size sorting method description of method m Method 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. false string MIXS:0000216 {text} sample size sorting method samp_time_out BuiltEnvInterface sampling time outside time hour 1 The recent and long term history of outside sampling false string MIXS:0000196 sampling time outside samp_weather BuiltEnvInterface sampling day weather enumeration 1 The weather on the sampling day foggy false samp_weather_enum MIXS:0000827 sampling day weather +sample_link BuiltEnvInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage season BuiltEnvInterface season NCIT:C94729 1 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). autumn [NCIT:C94733] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000829 {termLabel} {[termID]} season season_use BuiltEnvInterface seasonal use enumeration 1 The seasons the space is occupied Winter false season_use_enum MIXS:0000830 seasonal use shad_dev_water_mold BuiltEnvInterface shading device signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the shading device no presence of mold visible false string MIXS:0000834 [presence of mold visible|no presence of mold visible] shading device signs of water/mold @@ -847,8 +860,10 @@ shading_device_cond BuiltEnvInterface shading device condition enumeration 1 shading_device_loc BuiltEnvInterface shading device location enumeration 1 The location of the shading device in relation to the built structure exterior false string MIXS:0000832 [exterior|interior] shading device location shading_device_mat BuiltEnvInterface shading device material material name 1 The material the shading device is composed of false string MIXS:0000245 {text} shading device material shading_device_type BuiltEnvInterface shading device type enumeration 1 The type of shading device slatted aluminum awning false shading_device_type_enum MIXS:0000835 shading device type +size_frac BuiltEnvInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected space_typ_state BuiltEnvInterface space typical state enumeration 1 Customary or normal state of the space typically occupied false string MIXS:0000770 [typically occupied|typically unoccupied] space typical state specific BuiltEnvInterface specifications enumeration 1 The building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents construction false specific_enum MIXS:0000836 specifications +specific_ecosystem BuiltEnvInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true specific_humidity BuiltEnvInterface specific humidity measurement value gram of air, kilogram of air 1 The 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. 15 per kilogram of air false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000214 specific humidity substructure_type BuiltEnvInterface substructure type enumeration m The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level basement true substructure_type_enum MIXS:0000767 substructure type surf_air_cont BuiltEnvInterface surface-air contaminant enumeration m Contaminant identified on surface radon true surf_air_cont_enum MIXS:0000759 surface-air contaminant @@ -857,11 +872,13 @@ surf_material BuiltEnvInterface surface material enumeration 1 Surface materi surf_moisture BuiltEnvInterface surface moisture measurement value parts per million, gram per cubic meter, gram per square meter 1 Water held on a surface 0.01 gram per square meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000128 surface moisture surf_moisture_ph BuiltEnvInterface surface moisture pH measurement value 1 ph measurement of surface 7 false double MIXS:0000760 surface moisture pH surf_temp BuiltEnvInterface surface temperature measurement value degree Celsius 1 Temperature of the surface at the time of sampling 15 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000125 surface temperature +temp BuiltEnvInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature temp_out BuiltEnvInterface temperature outside house measurement value degree Celsius 1 The recorded temperature value at sampling time outside 5 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000197 temperature outside house train_line BuiltEnvInterface train line enumeration 1 The subway line name red false train_line_enum MIXS:0000837 train line train_stat_loc BuiltEnvInterface train station collection location enumeration 1 The train station collection location forest hills false train_stat_loc_enum MIXS:0000838 train station collection location train_stop_loc BuiltEnvInterface train stop collection location enumeration 1 The train stop collection location end false train_stop_loc_enum MIXS:0000839 train stop collection location typ_occup_density BuiltEnvInterface typical occupant density measurement value 1 Customary or normal density of occupants 25 false double MIXS:0000771 typical occupant density +ventilation_type BuiltEnvInterface ventilation type ventilation type name 1 Ventilation system used in the sampled premises Operable windows false string MIXS:0000756 {text} ventilation type vis_media BuiltEnvInterface visual media enumeration 1 The building visual media 3D scans false vis_media_enum MIXS:0000840 visual media wall_area BuiltEnvInterface wall area measurement value square meter 1 The total area of the sampled room's walls false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000198 wall area wall_const_type BuiltEnvInterface wall construction type enumeration 1 The building class of the wall defined by the composition of the building elements and fire-resistance rating. fire resistive false wall_const_type_enum MIXS:0000841 wall construction type @@ -886,111 +903,123 @@ window_status BuiltEnvInterface window status enumeration 1 Defines whether t window_type BuiltEnvInterface window type enumeration 1 The type of windows fixed window false window_type_enum MIXS:0000856 window type window_vert_pos BuiltEnvInterface window vertical position enumeration 1 The vertical position of the window on the wall middle false window_vert_pos_enum MIXS:0000857 window vertical position window_water_mold BuiltEnvInterface window signs of water/mold enumeration 1 Signs of the presence of mold or mildew on the window. no presence of mold visible false string MIXS:0000854 [presence of mold visible|no presence of mold visible] window signs of water/mold -size_frac BuiltEnvInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -collection_date BuiltEnvInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name BuiltEnvInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon BuiltEnvInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev BuiltEnvInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -depth BuiltEnvInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -alt BuiltEnvInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -experimental_factor BuiltEnvInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth BuiltEnvInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -temp BuiltEnvInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -analysis_type BuiltEnvInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package BuiltEnvInterface environmental package MIxS 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 mixs extension false string -sample_link BuiltEnvInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale BuiltEnvInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale BuiltEnvInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium BuiltEnvInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem BuiltEnvInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category BuiltEnvInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type BuiltEnvInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype BuiltEnvInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem BuiltEnvInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true oxy_stat_samp BuiltEnvInterface this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum rel_to_oxygen BuiltEnvInterface rel_to_oxygen_enum DhInterface One DataHarmonizer interface, for the specified combination of a checklist, enviornmental_package, and various standards, user facilities or analysis types Dh Root Interface DhMultiviewCommonColumnsMixin Mixin with DhMutliviewCommon Columns true Dh Mutliview Common Columns -samp_name DhMultiviewCommonColumnsMixin sample name text It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples. Rock core CB1178(5-6) from NSW false string true MIXS:0001107 {text} sample name -source_mat_id DhMultiviewCommonColumnsMixin Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).|Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). A globally unique identifier assigned to the biological sample. IGSN:AU1243|UUID:24f1467a-40f4-11ed-b878-0242ac120002 true false The source material IS the Globally Unique ID [^\:\n\r]+\:[^\:\n\r]+ string true MIXS:0000026 {text}:{text} globally unique ID Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.|Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. analysis_type DhMultiviewCommonColumnsMixin Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type env_package DhMultiviewCommonColumnsMixin environmental package MIxS 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 mixs extension false string +samp_name DhMultiviewCommonColumnsMixin sample name text It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples. Rock core CB1178(5-6) from NSW false string true MIXS:0001107 {text} sample name sample_link DhMultiviewCommonColumnsMixin This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage +source_mat_id DhMultiviewCommonColumnsMixin Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).|Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). A globally unique identifier assigned to the biological sample. IGSN:AU1243|UUID:24f1467a-40f4-11ed-b878-0242ac120002 true false The source material IS the Globally Unique ID [^\:\n\r]+\:[^\:\n\r]+ string true MIXS:0000026 {text}:{text} globally unique ID Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID.|Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. EmslInterface emsl dh_interface Emsl -project_id EmslInterface Proposal IDs or names associated with dataset false string true {text} project ID -sample_type EmslInterface This can vary from 'environmental package' if the sample is an extraction. Type of sample being submitted water extracted soil sample_type_enum true sample type -sample_shipped EmslInterface This field is only required when completing metadata for samples being submitted to EMSL for analyses. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. 15 g|100 uL|5 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true {float} {unit} sample shipped amount -emsl_store_temp EmslInterface Enter a temperature in celsius. Numeric portion only. The temperature at which the sample should be stored upon delivery to EMSL -80 float true {float} EMSL sample storage temperature, deg. C add 'see_alsos' with link to NEXUS info -technical_reps EmslInterface This field is only required when completing metadata for samples being submitted to EMSL for analyses. If sending technical replicates of the same sample, indicate the replicate count. 2 integer true {integer} number technical replicate -replicate_number EmslInterface This will guide staff in ensuring your samples are block & randomized correctly If sending biological replicates, indicate the rep number here. integer true {integer} replicate number analysis_type EmslInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type +emsl_store_temp EmslInterface Enter a temperature in celsius. Numeric portion only. The temperature at which the sample should be stored upon delivery to EMSL -80 float true {float} EMSL sample storage temperature, deg. C add 'see_alsos' with link to NEXUS info env_package EmslInterface environmental package MIxS 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 mixs extension false string +project_id EmslInterface Proposal IDs or names associated with dataset false string true {text} project ID +replicate_number EmslInterface This will guide staff in ensuring your samples are block & randomized correctly If sending biological replicates, indicate the rep number here. integer true {integer} replicate number sample_link EmslInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage +sample_shipped EmslInterface This field is only required when completing metadata for samples being submitted to EMSL for analyses. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL. 15 g|100 uL|5 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true {float} {unit} sample shipped amount +sample_type EmslInterface This can vary from 'environmental package' if the sample is an extraction. Type of sample being submitted water extracted soil sample_type_enum true sample type +technical_reps EmslInterface This field is only required when completing metadata for samples being submitted to EMSL for analyses. If sending technical replicates of the same sample, indicate the replicate count. 2 integer true {integer} number technical replicate HcrCoresInterface hcr_cores dh_interface Hcr Cores +additional_info HcrCoresInterface additional info text 1 Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary false string MIXS:0000300 {text} additional info alkalinity HcrCoresInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity -ammonium HcrCoresInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium -calcium HcrCoresInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium -chloride HcrCoresInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride -density HcrCoresInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density -diss_carb_dioxide HcrCoresInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide -diss_inorg_carb HcrCoresInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon -diss_org_carb HcrCoresInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon -magnesium HcrCoresInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium -nitrate HcrCoresInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate -nitrite HcrCoresInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite -organism_count HcrCoresInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -porosity HcrCoresInterface porosity measurement value or range percentage 1 Porosity of deposited sediment is volume of voids divided by the total volume of sample false string MIXS:0000211 {float} - {float} {unit} porosity -potassium HcrCoresInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium -pressure HcrCoresInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure -samp_store_loc HcrCoresInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location -sulfate HcrCoresInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate alkalinity_method HcrCoresInterface alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method -diss_inorg_phosp HcrCoresInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus -size_frac HcrCoresInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -additional_info HcrCoresInterface additional info text 1 Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary false string MIXS:0000300 {text} additional info +alt HcrCoresInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +ammonium HcrCoresInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type HcrCoresInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type api HcrCoresInterface API gravity measurement value degrees API 1 API 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¬∞ API) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000157 API gravity aromatics_pc HcrCoresInterface aromatics wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000133 {text};{float} {unit} aromatics wt% asphaltenes_pc HcrCoresInterface asphaltenes wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000135 {text};{float} {unit} asphaltenes wt% basin HcrCoresInterface basin name name 1 Name of the basin (e.g. Campos) false string MIXS:0000290 {text} basin name benzene HcrCoresInterface benzene measurement value milligram per liter, parts per million 1 Concentration of benzene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000153 benzene +calcium HcrCoresInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +chem_administration HcrCoresInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration +chloride HcrCoresInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride +collection_date HcrCoresInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +density HcrCoresInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density depos_env HcrCoresInterface depositional environment enumeration 1 "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If ""other"" is specified, please propose entry in ""additional info"" field" Continental - Alluvial false depos_env_enum MIXS:0000992 depositional environment +depth HcrCoresInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters +diss_carb_dioxide HcrCoresInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide +diss_inorg_carb HcrCoresInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon +diss_inorg_phosp HcrCoresInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus diss_iron HcrCoresInterface dissolved iron measurement value milligram per liter 1 Concentration of dissolved iron in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000139 dissolved iron +diss_org_carb HcrCoresInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon diss_oxygen_fluid HcrCoresInterface dissolved oxygen in fluids measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000438 dissolved oxygen in fluids +ecosystem HcrCoresInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category HcrCoresInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype HcrCoresInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type HcrCoresInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev HcrCoresInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale HcrCoresInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale HcrCoresInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium HcrCoresInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package HcrCoresInterface environmental package MIxS 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 mixs extension false string ethylbenzene HcrCoresInterface ethylbenzene measurement value milligram per liter, parts per million 1 Concentration of ethylbenzene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000155 ethylbenzene +experimental_factor HcrCoresInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor field HcrCoresInterface field name name 1 Name of the hydrocarbon field (e.g. Albacora) false string MIXS:0000291 {text} field name +geo_loc_name HcrCoresInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) hc_produced HcrCoresInterface hydrocarbon type produced enumeration 1 "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If ""other"" is specified, please propose entry in ""additional info"" field" Gas false hc_produced_enum MIXS:0000989 hydrocarbon type produced hcr HcrCoresInterface hydrocarbon resource type enumeration 1 "Main 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" Oil Sand false hcr_enum MIXS:0000988 hydrocarbon resource type hcr_fw_salinity HcrCoresInterface formation water salinity measurement value milligram per liter 1 Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000406 formation water salinity hcr_geol_age HcrCoresInterface hydrocarbon resource geological age enumeration 1 "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false hcr_geol_age_enum MIXS:0000993 hydrocarbon resource geological age hcr_pressure HcrCoresInterface hydrocarbon resource original pressure measurement value range atmosphere, kilopascal 1 Original pressure of the hydrocarbon resource false string MIXS:0000395 {float} - {float} {unit} hydrocarbon resource original pressure hcr_temp HcrCoresInterface hydrocarbon resource original temperature measurement value range degree Celsius 1 Original temperature of the hydrocarbon resource 150-295 degree Celsius false string MIXS:0000393 {float} - {float} {unit} hydrocarbon resource original temperature +horizon_meth HcrCoresInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +lat_lon HcrCoresInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) lithology HcrCoresInterface lithology enumeration 1 "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If ""other"" is specified, please propose entry in ""additional info"" field" Volcanic false lithology_enum MIXS:0000990 lithology +magnesium HcrCoresInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium +misc_param HcrCoresInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +nitrate HcrCoresInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate +nitrite HcrCoresInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite org_count_qpcr_info HcrCoresInterface organism count qPCR information gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles number of cells per gram (or ml or cm^2) 1 If 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) false string MIXS:0000099 {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles organism count qPCR information +organism_count HcrCoresInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count owc_tvdss HcrCoresInterface oil water contact depth measurement value meter 1 Depth of the original oil water contact (OWC) zone (average) (m TVDSS) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000405 oil water contact depth +oxy_stat_samp HcrCoresInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample permeability HcrCoresInterface permeability measurement value range mD 1 Measure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences)) false string MIXS:0000404 {integer} - {integer} {unit} permeability +ph HcrCoresInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth HcrCoresInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method +porosity HcrCoresInterface porosity measurement value or range percentage 1 Porosity of deposited sediment is volume of voids divided by the total volume of sample false string MIXS:0000211 {float} - {float} {unit} porosity +potassium HcrCoresInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pour_point HcrCoresInterface pour point measurement value degree Celsius 1 Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is 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) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000127 pour point +pressure HcrCoresInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure +rel_to_oxygen HcrCoresInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen reservoir HcrCoresInterface reservoir name name 1 Name of the reservoir (e.g. Carapebus) false string MIXS:0000303 {text} reservoir name resins_pc HcrCoresInterface resins wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000134 {text};{float} {unit} resins wt% +salinity HcrCoresInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device HcrCoresInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method HcrCoresInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process HcrCoresInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing samp_md HcrCoresInterface sample measured depth measurement value;enumeration meter 1 "In 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" 1534 meter;MSL false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000413 sample measured depth +samp_size HcrCoresInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected samp_store_dur HcrCoresInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc HcrCoresInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp HcrCoresInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature samp_subtype HcrCoresInterface sample subtype enumeration 1 "Name 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" biofilm false samp_subtype_enum MIXS:0000999 sample subtype samp_transport_cond HcrCoresInterface sample transport conditions measurement value;measurement value days;degree Celsius 1 Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) 5 days;-20 degree Celsius false string MIXS:0000410 {float} {unit};{float} {unit} sample transport conditions samp_tvdss HcrCoresInterface sample true vertical depth subsea measurement value or measurement value range meter 1 Depth 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 false string MIXS:0000409 {float}-{float} {unit} sample true vertical depth subsea samp_type HcrCoresInterface sample type GENEPIO:0001246 1 The 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). built environment sample [GENEPIO:0001248] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000998 {termLabel} {[termID]} sample type samp_well_name HcrCoresInterface sample well name name 1 Name of the well (e.g. BXA1123) where sample was taken false string MIXS:0000296 {text} sample well name +sample_link HcrCoresInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage saturates_pc HcrCoresInterface saturates wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000131 {text};{float} {unit} saturates wt% +size_frac HcrCoresInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected sodium HcrCoresInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium +specific_ecosystem HcrCoresInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true sr_dep_env HcrCoresInterface source rock depositional environment enumeration 1 "Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If ""other"" is specified, please propose entry in ""additional info"" field" Marine false sr_dep_env_enum MIXS:0000996 source rock depositional environment sr_geol_age HcrCoresInterface source rock geological age enumeration 1 "Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false sr_geol_age_enum MIXS:0000997 source rock geological age sr_kerog_type HcrCoresInterface source rock kerogen type enumeration 1 "Origin 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" Type IV false sr_kerog_type_enum MIXS:0000994 source rock kerogen type sr_lithology HcrCoresInterface source rock lithology enumeration 1 "Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If ""other"" is specified, please propose entry in ""additional info"" field" Coal false sr_lithology_enum MIXS:0000995 source rock lithology +sulfate HcrCoresInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate sulfate_fw HcrCoresInterface sulfate in formation water measurement value milligram per liter 1 Original sulfate concentration in the hydrocarbon resource false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000407 sulfate in formation water sulfide HcrCoresInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide suspend_solids HcrCoresInterface suspended solids suspended solid name;measurement value gram, microgram, milligram per liter, mole per liter, gram per liter, part per million m Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000150 {text};{float} {unit} suspended solids tan HcrCoresInterface total acid number measurement value milligram per liter 1 Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000120 total acid number +temp HcrCoresInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature toluene HcrCoresInterface toluene measurement value milligram per liter, parts per million 1 Concentration of toluene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000154 toluene tot_iron HcrCoresInterface total iron measurement value milligram per liter, milligram per kilogram 1 Concentration of total iron in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000105 total iron tot_nitro HcrCoresInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration +tot_phosp HcrCoresInterface total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000117 total phosphorus tot_sulfur HcrCoresInterface total sulfur measurement value milligram per liter, parts per million 1 Concentration of total sulfur in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000419 total sulfur tvdss_of_hcr_press HcrCoresInterface depth (TVDSS) of hydrocarbon resource pressure measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000397 depth (TVDSS) of hydrocarbon resource pressure tvdss_of_hcr_temp HcrCoresInterface depth (TVDSS) of hydrocarbon resource temperature measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000394 depth (TVDSS) of hydrocarbon resource temperature @@ -999,61 +1028,14 @@ vfa_fw HcrCoresInterface vfa in formation water measurement value milligram per viscosity HcrCoresInterface viscosity measurement value;measurement value cP at degree Celsius 1 A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) false string MIXS:0000126 {float} {unit};{float} {unit} viscosity win HcrCoresInterface well identification number text 1 A 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) false string MIXS:0000297 {text} well identification number xylene HcrCoresInterface xylene measurement value milligram per liter, parts per million 1 Concentration of xylene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000156 xylene -collection_date HcrCoresInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name HcrCoresInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon HcrCoresInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev HcrCoresInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp HcrCoresInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth HcrCoresInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process HcrCoresInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device HcrCoresInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method HcrCoresInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration HcrCoresInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size HcrCoresInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen HcrCoresInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt HcrCoresInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph HcrCoresInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor HcrCoresInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth HcrCoresInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param HcrCoresInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp HcrCoresInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp HcrCoresInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -ph_meth HcrCoresInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -tot_phosp HcrCoresInterface total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000117 total phosphorus -salinity HcrCoresInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type HcrCoresInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package HcrCoresInterface environmental package MIxS 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 mixs extension false string -sample_link HcrCoresInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale HcrCoresInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale HcrCoresInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium HcrCoresInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem HcrCoresInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category HcrCoresInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type HcrCoresInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype HcrCoresInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem HcrCoresInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true HcrFluidsSwabsInterface hcr_fluids_swabs dh_interface Hcr Fluids Swabs -alkalinity HcrFluidsSwabsInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity -ammonium HcrFluidsSwabsInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium -calcium HcrFluidsSwabsInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium -chloride HcrFluidsSwabsInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride -density HcrFluidsSwabsInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density -diss_carb_dioxide HcrFluidsSwabsInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide -diss_inorg_carb HcrFluidsSwabsInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon -diss_org_carb HcrFluidsSwabsInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon -magnesium HcrFluidsSwabsInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium -nitrate HcrFluidsSwabsInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate -nitrite HcrFluidsSwabsInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite -organism_count HcrFluidsSwabsInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -potassium HcrFluidsSwabsInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium -pressure HcrFluidsSwabsInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure -samp_store_loc HcrFluidsSwabsInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location -sulfate HcrFluidsSwabsInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate -alkalinity_method HcrFluidsSwabsInterface alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method -diss_inorg_phosp HcrFluidsSwabsInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus -size_frac HcrFluidsSwabsInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected add_recov_method HcrFluidsSwabsInterface secondary and tertiary recovery methods and start date enumeration;timestamp 1 "Additional (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" Polymer Addition;2018-06-21T14:30Z false string MIXS:0001009 secondary and tertiary recovery methods and start date additional_info HcrFluidsSwabsInterface additional info text 1 Information that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary false string MIXS:0000300 {text} additional info +alkalinity HcrFluidsSwabsInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity +alkalinity_method HcrFluidsSwabsInterface alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method +alt HcrFluidsSwabsInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +ammonium HcrFluidsSwabsInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type HcrFluidsSwabsInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type api HcrFluidsSwabsInterface API gravity measurement value degrees API 1 API 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¬∞ API) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000157 API gravity aromatics_pc HcrFluidsSwabsInterface aromatics wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000133 {text};{float} {unit} aromatics wt% asphaltenes_pc HcrFluidsSwabsInterface asphaltenes wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000135 {text};{float} {unit} asphaltenes wt% @@ -1061,286 +1043,315 @@ basin HcrFluidsSwabsInterface basin name name 1 Name of the basin (e.g. Campo benzene HcrFluidsSwabsInterface benzene measurement value milligram per liter, parts per million 1 Concentration of benzene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000153 benzene biocide HcrFluidsSwabsInterface biocide administration name;name;timestamp 1 List of biocides (commercial name of product and supplier) and date of administration ALPHA 1427;Baker Hughes;2008-01-23 false string MIXS:0001011 {text};{text};{timestamp} biocide administration biocide_admin_method HcrFluidsSwabsInterface biocide administration method measurement value;frequency;duration;duration milligram per liter 1 Method of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days) false string MIXS:0000456 {float} {unit};{Rn/start_time/end_time/duration};{duration} biocide administration method +calcium HcrFluidsSwabsInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +chem_administration HcrFluidsSwabsInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chem_treat_method HcrFluidsSwabsInterface chemical treatment method measurement value;frequency;duration;duration milligram per liter 1 Method of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days) false string MIXS:0000457 {float} {unit};{Rn/start_time/end_time/duration};{duration};{duration} chemical treatment method chem_treatment HcrFluidsSwabsInterface chemical treatment name;name;timestamp 1 List 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 ACCENT 1125;DOW;2010-11-17 false string MIXS:0001012 {text};{text};{timestamp} chemical treatment +chloride HcrFluidsSwabsInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride +collection_date HcrFluidsSwabsInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +density HcrFluidsSwabsInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density depos_env HcrFluidsSwabsInterface depositional environment enumeration 1 "Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If ""other"" is specified, please propose entry in ""additional info"" field" Continental - Alluvial false depos_env_enum MIXS:0000992 depositional environment +depth HcrFluidsSwabsInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters +diss_carb_dioxide HcrFluidsSwabsInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide +diss_inorg_carb HcrFluidsSwabsInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon +diss_inorg_phosp HcrFluidsSwabsInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus diss_iron HcrFluidsSwabsInterface dissolved iron measurement value milligram per liter 1 Concentration of dissolved iron in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000139 dissolved iron +diss_org_carb HcrFluidsSwabsInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon diss_oxygen_fluid HcrFluidsSwabsInterface dissolved oxygen in fluids measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000438 dissolved oxygen in fluids +ecosystem HcrFluidsSwabsInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category HcrFluidsSwabsInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype HcrFluidsSwabsInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type HcrFluidsSwabsInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev HcrFluidsSwabsInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale HcrFluidsSwabsInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale HcrFluidsSwabsInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium HcrFluidsSwabsInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package HcrFluidsSwabsInterface environmental package MIxS 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 mixs extension false string ethylbenzene HcrFluidsSwabsInterface ethylbenzene measurement value milligram per liter, parts per million 1 Concentration of ethylbenzene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000155 ethylbenzene +experimental_factor HcrFluidsSwabsInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor field HcrFluidsSwabsInterface field name name 1 Name of the hydrocarbon field (e.g. Albacora) false string MIXS:0000291 {text} field name +geo_loc_name HcrFluidsSwabsInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) hc_produced HcrFluidsSwabsInterface hydrocarbon type produced enumeration 1 "Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If ""other"" is specified, please propose entry in ""additional info"" field" Gas false hc_produced_enum MIXS:0000989 hydrocarbon type produced hcr HcrFluidsSwabsInterface hydrocarbon resource type enumeration 1 "Main 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" Oil Sand false hcr_enum MIXS:0000988 hydrocarbon resource type hcr_fw_salinity HcrFluidsSwabsInterface formation water salinity measurement value milligram per liter 1 Original formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000406 formation water salinity hcr_geol_age HcrFluidsSwabsInterface hydrocarbon resource geological age enumeration 1 "Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If ""other"" is specified, please propose entry in ""additional info"" field" Silurian false hcr_geol_age_enum MIXS:0000993 hydrocarbon resource geological age hcr_pressure HcrFluidsSwabsInterface hydrocarbon resource original pressure measurement value range atmosphere, kilopascal 1 Original pressure of the hydrocarbon resource false string MIXS:0000395 {float} - {float} {unit} hydrocarbon resource original pressure hcr_temp HcrFluidsSwabsInterface hydrocarbon resource original temperature measurement value range degree Celsius 1 Original temperature of the hydrocarbon resource 150-295 degree Celsius false string MIXS:0000393 {float} - {float} {unit} hydrocarbon resource original temperature +horizon_meth HcrFluidsSwabsInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method iw_bt_date_well HcrFluidsSwabsInterface injection water breakthrough date of specific well timestamp 1 Injection water breakthrough date per well following a secondary and/or tertiary recovery 2018-05-11 false string MIXS:0001010 injection water breakthrough date of specific well iwf HcrFluidsSwabsInterface injection water fraction measurement value percent 1 Proportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000455 injection water fraction +lat_lon HcrFluidsSwabsInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) lithology HcrFluidsSwabsInterface lithology enumeration 1 "Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If ""other"" is specified, please propose entry in ""additional info"" field" Volcanic false lithology_enum MIXS:0000990 lithology +magnesium HcrFluidsSwabsInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium +misc_param HcrFluidsSwabsInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +nitrate HcrFluidsSwabsInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate +nitrite HcrFluidsSwabsInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite org_count_qpcr_info HcrFluidsSwabsInterface organism count qPCR information gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles number of cells per gram (or ml or cm^2) 1 If 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) false string MIXS:0000099 {text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes; total cycles organism count qPCR information +organism_count HcrFluidsSwabsInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp HcrFluidsSwabsInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample +ph HcrFluidsSwabsInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth HcrFluidsSwabsInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method +potassium HcrFluidsSwabsInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pour_point HcrFluidsSwabsInterface pour point measurement value degree Celsius 1 Temperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high¬†pour point¬†is 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) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000127 pour point +pressure HcrFluidsSwabsInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure prod_rate HcrFluidsSwabsInterface production rate measurement value cubic meter per day 1 Oil and/or gas production rates per well (e.g. 524 m3 / day) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000452 production rate prod_start_date HcrFluidsSwabsInterface production start date timestamp 1 Date of field's first production 2018-05-11 false string MIXS:0001008 production start date +rel_to_oxygen HcrFluidsSwabsInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen reservoir HcrFluidsSwabsInterface reservoir name name 1 Name of the reservoir (e.g. Carapebus) false string MIXS:0000303 {text} reservoir name resins_pc HcrFluidsSwabsInterface resins wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000134 {text};{float} {unit} resins wt% +salinity HcrFluidsSwabsInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device HcrFluidsSwabsInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method HcrFluidsSwabsInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method samp_collect_point HcrFluidsSwabsInterface sample collection point enumeration 1 "Sampling 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" well false samp_collect_point_enum MIXS:0001015 sample collection point samp_loc_corr_rate HcrFluidsSwabsInterface corrosion rate at sample location measurement value range millimeter per year 1 Metal 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 false string MIXS:0000136 {float} - {float} {unit} corrosion rate at sample location +samp_mat_process HcrFluidsSwabsInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing samp_preserv HcrFluidsSwabsInterface preservative added to sample name;measurement value milliliter 1 Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000463 {text};{float} {unit} preservative added to sample +samp_size HcrFluidsSwabsInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected samp_store_dur HcrFluidsSwabsInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc HcrFluidsSwabsInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp HcrFluidsSwabsInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature samp_subtype HcrFluidsSwabsInterface sample subtype enumeration 1 "Name 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" biofilm false samp_subtype_enum MIXS:0000999 sample subtype samp_transport_cond HcrFluidsSwabsInterface sample transport conditions measurement value;measurement value days;degree Celsius 1 Sample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 ¬∞C) 5 days;-20 degree Celsius false string MIXS:0000410 {float} {unit};{float} {unit} sample transport conditions samp_type HcrFluidsSwabsInterface sample type GENEPIO:0001246 1 The 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). built environment sample [GENEPIO:0001248] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000998 {termLabel} {[termID]} sample type samp_well_name HcrFluidsSwabsInterface sample well name name 1 Name of the well (e.g. BXA1123) where sample was taken false string MIXS:0000296 {text} sample well name -saturates_pc HcrFluidsSwabsInterface saturates wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000131 {text};{float} {unit} saturates wt% -sodium HcrFluidsSwabsInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium -sulfate_fw HcrFluidsSwabsInterface sulfate in formation water measurement value milligram per liter 1 Original sulfate concentration in the hydrocarbon resource false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000407 sulfate in formation water -sulfide HcrFluidsSwabsInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide -suspend_solids HcrFluidsSwabsInterface suspended solids suspended solid name;measurement value gram, microgram, milligram per liter, mole per liter, gram per liter, part per million m Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000150 {text};{float} {unit} suspended solids -tan HcrFluidsSwabsInterface total acid number measurement value milligram per liter 1 Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000120 total acid number -toluene HcrFluidsSwabsInterface toluene measurement value milligram per liter, parts per million 1 Concentration of toluene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000154 toluene -tot_iron HcrFluidsSwabsInterface total iron measurement value milligram per liter, milligram per kilogram 1 Concentration of total iron in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000105 total iron -tot_nitro HcrFluidsSwabsInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration -tot_sulfur HcrFluidsSwabsInterface total sulfur measurement value milligram per liter, parts per million 1 Concentration of total sulfur in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000419 total sulfur -tvdss_of_hcr_press HcrFluidsSwabsInterface depth (TVDSS) of hydrocarbon resource pressure measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000397 depth (TVDSS) of hydrocarbon resource pressure -tvdss_of_hcr_temp HcrFluidsSwabsInterface depth (TVDSS) of hydrocarbon resource temperature measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000394 depth (TVDSS) of hydrocarbon resource temperature -vfa HcrFluidsSwabsInterface volatile fatty acids measurement value milligram per liter, parts per million 1 Concentration of Volatile Fatty Acids in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000152 volatile fatty acids -vfa_fw HcrFluidsSwabsInterface vfa in formation water measurement value milligram per liter 1 Original volatile fatty acid concentration in the hydrocarbon resource false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000408 vfa in formation water -viscosity HcrFluidsSwabsInterface viscosity measurement value;measurement value cP at degree Celsius 1 A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) false string MIXS:0000126 {float} {unit};{float} {unit} viscosity -water_cut HcrFluidsSwabsInterface water cut measurement value percent 1 Current amount of water (%) in a produced fluid stream; or the average of the combined streams false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000454 water cut -water_prod_rate HcrFluidsSwabsInterface water production rate measurement value cubic meter per day 1 Water production rates per well (e.g. 987 m3 / day) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000453 water production rate -win HcrFluidsSwabsInterface well identification number text 1 A 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) false string MIXS:0000297 {text} well identification number -xylene HcrFluidsSwabsInterface xylene measurement value milligram per liter, parts per million 1 Concentration of xylene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000156 xylene -collection_date HcrFluidsSwabsInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name HcrFluidsSwabsInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon HcrFluidsSwabsInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev HcrFluidsSwabsInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp HcrFluidsSwabsInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth HcrFluidsSwabsInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process HcrFluidsSwabsInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device HcrFluidsSwabsInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method HcrFluidsSwabsInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration HcrFluidsSwabsInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size HcrFluidsSwabsInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen HcrFluidsSwabsInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt HcrFluidsSwabsInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph HcrFluidsSwabsInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor HcrFluidsSwabsInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth HcrFluidsSwabsInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param HcrFluidsSwabsInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp HcrFluidsSwabsInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp HcrFluidsSwabsInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -ph_meth HcrFluidsSwabsInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -tot_phosp HcrFluidsSwabsInterface total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000117 total phosphorus -salinity HcrFluidsSwabsInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type HcrFluidsSwabsInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package HcrFluidsSwabsInterface environmental package MIxS 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 mixs extension false string sample_link HcrFluidsSwabsInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale HcrFluidsSwabsInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale HcrFluidsSwabsInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium HcrFluidsSwabsInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem HcrFluidsSwabsInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category HcrFluidsSwabsInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type HcrFluidsSwabsInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype HcrFluidsSwabsInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +saturates_pc HcrFluidsSwabsInterface saturates wt% name;measurement value percent 1 Saturate, Aromatic, Resin and Asphaltene¬†(SARA) is an analysis method that divides¬†crude oil¬†components 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) false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000131 {text};{float} {unit} saturates wt% +size_frac HcrFluidsSwabsInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +sodium HcrFluidsSwabsInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium specific_ecosystem HcrFluidsSwabsInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +sulfate HcrFluidsSwabsInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate +sulfate_fw HcrFluidsSwabsInterface sulfate in formation water measurement value milligram per liter 1 Original sulfate concentration in the hydrocarbon resource false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000407 sulfate in formation water +sulfide HcrFluidsSwabsInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide +suspend_solids HcrFluidsSwabsInterface suspended solids suspended solid name;measurement value gram, microgram, milligram per liter, mole per liter, gram per liter, part per million m Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000150 {text};{float} {unit} suspended solids +tan HcrFluidsSwabsInterface total acid number measurement value milligram per liter 1 Total Acid Number¬†(TAN) is a measurement of acidity that is determined by the amount of¬†potassium hydroxide¬†in milligrams that is needed to neutralize the acids in one gram of oil.¬†It is an important quality measurement of¬†crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000120 total acid number +temp HcrFluidsSwabsInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature +toluene HcrFluidsSwabsInterface toluene measurement value milligram per liter, parts per million 1 Concentration of toluene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000154 toluene +tot_iron HcrFluidsSwabsInterface total iron measurement value milligram per liter, milligram per kilogram 1 Concentration of total iron in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000105 total iron +tot_nitro HcrFluidsSwabsInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration +tot_phosp HcrFluidsSwabsInterface total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000117 total phosphorus +tot_sulfur HcrFluidsSwabsInterface total sulfur measurement value milligram per liter, parts per million 1 Concentration of total sulfur in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000419 total sulfur +tvdss_of_hcr_press HcrFluidsSwabsInterface depth (TVDSS) of hydrocarbon resource pressure measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000397 depth (TVDSS) of hydrocarbon resource pressure +tvdss_of_hcr_temp HcrFluidsSwabsInterface depth (TVDSS) of hydrocarbon resource temperature measurement value meter 1 True vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m). false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000394 depth (TVDSS) of hydrocarbon resource temperature +vfa HcrFluidsSwabsInterface volatile fatty acids measurement value milligram per liter, parts per million 1 Concentration of Volatile Fatty Acids in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000152 volatile fatty acids +vfa_fw HcrFluidsSwabsInterface vfa in formation water measurement value milligram per liter 1 Original volatile fatty acid concentration in the hydrocarbon resource false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000408 vfa in formation water +viscosity HcrFluidsSwabsInterface viscosity measurement value;measurement value cP at degree Celsius 1 A measure of oil's resistance¬†to gradual deformation by¬†shear stress¬†or¬†tensile stress (e.g. 3.5 cp; 100 ¬∞C) false string MIXS:0000126 {float} {unit};{float} {unit} viscosity +water_cut HcrFluidsSwabsInterface water cut measurement value percent 1 Current amount of water (%) in a produced fluid stream; or the average of the combined streams false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000454 water cut +water_prod_rate HcrFluidsSwabsInterface water production rate measurement value cubic meter per day 1 Water production rates per well (e.g. 987 m3 / day) false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000453 water production rate +win HcrFluidsSwabsInterface well identification number text 1 A 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) false string MIXS:0000297 {text} well identification number +xylene HcrFluidsSwabsInterface xylene measurement value milligram per liter, parts per million 1 Concentration of xylene in the sample false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000156 xylene HostAssociatedInterface host_associated dh_interface Host Associated -organism_count HostAssociatedInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -perturbation HostAssociatedInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation -samp_store_loc HostAssociatedInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +alt HostAssociatedInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +analysis_type HostAssociatedInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type ances_data HostAssociatedInterface ancestral data free text 1 Information 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) A/3*B false string MIXS:0000247 {text} ancestral data biol_stat HostAssociatedInterface biological status enumeration 1 The level of genome modification. natural false biol_stat_enum MIXS:0000858 biological status -genetic_mod HostAssociatedInterface genetic modification PMID,DOI,url or free text 1 Genetic 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 aox1A transgenic false string MIXS:0000859 {PMID}|{DOI}|{URL}|{text} genetic modification -host_age HostAssociatedInterface host age value year, day, hour 1 Age 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 10 days false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000255 host age -host_common_name HostAssociatedInterface host common name common name 1 Common name of the host. human false string MIXS:0000248 {text} host common name -host_dry_mass HostAssociatedInterface host dry mass measurement value kilogram, gram 1 Measurement of dry mass 500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000257 host dry mass -host_genotype HostAssociatedInterface host genotype genotype 1 Observed genotype C57BL/6 false string MIXS:0000365 {text} host genotype -host_height HostAssociatedInterface host height measurement value centimeter, millimeter, meter 1 The height of subject 0.1 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000264 host height -host_length HostAssociatedInterface host length measurement value centimeter, millimeter, meter 1 The length of subject 1 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000256 host length -host_life_stage HostAssociatedInterface host life stage stage 1 Description of life stage of host adult false string MIXS:0000251 {text} host life stage -host_phenotype HostAssociatedInterface host phenotype PATO or HP 1 Phenotype 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 elongated [PATO:0001154] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000874 {termLabel} {[termID]} host phenotype -host_subspecf_genlin HostAssociatedInterface host subspecific genetic lineage Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar. m Information 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. serovar:Newport, variety:glabrum, cultivar: Red Delicious false string MIXS:0001318 {rank name}:{text} host subspecific genetic lineage -host_symbiont HostAssociatedInterface observed host symbionts species name or common name m The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. flukeworms false string MIXS:0001298 {text} observed host symbionts -host_taxid HostAssociatedInterface host taxid NCBI taxon identifier 1 NCBI taxon id of the host, e.g. 9606 7955 false string MIXS:0000250 {NCBI taxid} host taxid -host_tot_mass HostAssociatedInterface host total mass measurement value kilogram, gram 1 Total mass of the host at collection, the unit depends on host 2500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000263 host total mass -samp_capt_status HostAssociatedInterface sample capture status enumeration 1 Reason for the sample farm sample false samp_capt_status_enum MIXS:0000860 sample capture status -samp_dis_stage HostAssociatedInterface sample disease stage enumeration 1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. infection false samp_dis_stage_enum MIXS:0000249 sample disease stage -size_frac HostAssociatedInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected blood_press_diast HostAssociatedInterface host blood pressure diastolic measurement value millimeter mercury 1 Resting diastolic blood pressure, measured as mm mercury false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000258 host blood pressure diastolic blood_press_syst HostAssociatedInterface host blood pressure systolic measurement value millimeter mercury 1 Resting systolic blood pressure, measured as mm mercury false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000259 host blood pressure systolic +chem_administration HostAssociatedInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration +collection_date HostAssociatedInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +depth HostAssociatedInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters +ecosystem HostAssociatedInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category HostAssociatedInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype HostAssociatedInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type HostAssociatedInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev HostAssociatedInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale HostAssociatedInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale HostAssociatedInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium HostAssociatedInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package HostAssociatedInterface environmental package MIxS 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 mixs extension false string +experimental_factor HostAssociatedInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +genetic_mod HostAssociatedInterface genetic modification PMID,DOI,url or free text 1 Genetic 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 aox1A transgenic false string MIXS:0000859 {PMID}|{DOI}|{URL}|{text} genetic modification +geo_loc_name HostAssociatedInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) gravidity HostAssociatedInterface gravidity gravidity status;timestamp 1 Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used yes;due date:2018-05-11 false string MIXS:0000875 {boolean};{timestamp} gravidity +horizon_meth HostAssociatedInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +host_age HostAssociatedInterface host age value year, day, hour 1 Age 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 10 days false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000255 host age host_body_habitat HostAssociatedInterface host body habitat free text 1 Original body habitat where the sample was obtained from nasopharynx false string MIXS:0000866 {text} host body habitat host_body_product HostAssociatedInterface host body product FMA or UBERON 1 Substance 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 Portion of mucus [fma66938] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000888 {termLabel} {[termID]} host body product host_body_site HostAssociatedInterface host body site FMA or UBERON 1 Name 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 gill [UBERON:0002535] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000867 {termLabel} {[termID]} host body site host_body_temp HostAssociatedInterface host body temperature measurement value degree Celsius 1 Core body temperature of the host when sample was collected 15 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000274 host body temperature host_color HostAssociatedInterface host color color 1 The color of host false string MIXS:0000260 {text} host color +host_common_name HostAssociatedInterface host common name common name 1 Common name of the host. human false string MIXS:0000248 {text} host common name host_diet HostAssociatedInterface host diet diet type m Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types herbivore false string MIXS:0000869 {text} host diet +host_dry_mass HostAssociatedInterface host dry mass measurement value kilogram, gram 1 Measurement of dry mass 500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000257 host dry mass host_family_relation HostAssociatedInterface host family relationship relationship type;arbitrary identifier m Familial relationships to other hosts in the same study; can include multiple relationships offspring;Mussel25 false string MIXS:0000872 {text};{text} host family relationship +host_genotype HostAssociatedInterface host genotype genotype 1 Observed genotype C57BL/6 false string MIXS:0000365 {text} host genotype host_growth_cond HostAssociatedInterface host growth conditions PMID,DOI,url or free text 1 Literature reference giving growth conditions of the host https://academic.oup.com/icesjms/article/68/2/349/617247 false string MIXS:0000871 {PMID}|{DOI}|{URL}|{text} host growth conditions +host_height HostAssociatedInterface host height measurement value centimeter, millimeter, meter 1 The height of subject 0.1 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000264 host height host_last_meal HostAssociatedInterface host last meal content;duration m Content of last meal and time since feeding; can include multiple values corn feed;P2H false string MIXS:0000870 {text};{duration} host last meal +host_length HostAssociatedInterface host length measurement value centimeter, millimeter, meter 1 The length of subject 1 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000256 host length +host_life_stage HostAssociatedInterface host life stage stage 1 Description of life stage of host adult false string MIXS:0000251 {text} host life stage +host_phenotype HostAssociatedInterface host phenotype PATO or HP 1 Phenotype 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 elongated [PATO:0001154] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000874 {termLabel} {[termID]} host phenotype host_sex HostAssociatedInterface host sex enumeration 1 Gender or physical sex of the host. non-binary false host_sex_enum MIXS:0000811 host sex host_shape HostAssociatedInterface host shape shape 1 Morphological shape of host round false string MIXS:0000261 {text} host shape host_subject_id HostAssociatedInterface host subject id unique identifier 1 A unique identifier by which each subject can be referred to, de-identified. MPI123 false string MIXS:0000861 {text} host subject id +host_subspecf_genlin HostAssociatedInterface host subspecific genetic lineage Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar. m Information 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. serovar:Newport, variety:glabrum, cultivar: Red Delicious false string MIXS:0001318 {rank name}:{text} host subspecific genetic lineage host_substrate HostAssociatedInterface host substrate substrate name 1 The growth substrate of the host. rock false string MIXS:0000252 {text} host substrate -samp_store_dur HostAssociatedInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration -collection_date HostAssociatedInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name HostAssociatedInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) +host_symbiont HostAssociatedInterface observed host symbionts species name or common name m The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. flukeworms false string MIXS:0001298 {text} observed host symbionts +host_taxid HostAssociatedInterface host taxid NCBI taxon identifier 1 NCBI taxon id of the host, e.g. 9606 7955 false string MIXS:0000250 {NCBI taxid} host taxid +host_tot_mass HostAssociatedInterface host total mass measurement value kilogram, gram 1 Total mass of the host at collection, the unit depends on host 2500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000263 host total mass lat_lon HostAssociatedInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev HostAssociatedInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp HostAssociatedInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth HostAssociatedInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process HostAssociatedInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device HostAssociatedInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method HostAssociatedInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration HostAssociatedInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size HostAssociatedInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen HostAssociatedInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt HostAssociatedInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -experimental_factor HostAssociatedInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth HostAssociatedInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method misc_param HostAssociatedInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +organism_count HostAssociatedInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count oxy_stat_samp HostAssociatedInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp HostAssociatedInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature +perturbation HostAssociatedInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation +rel_to_oxygen HostAssociatedInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen salinity HostAssociatedInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type HostAssociatedInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package HostAssociatedInterface environmental package MIxS 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 mixs extension false string +samp_capt_status HostAssociatedInterface sample capture status enumeration 1 Reason for the sample farm sample false samp_capt_status_enum MIXS:0000860 sample capture status +samp_collec_device HostAssociatedInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method HostAssociatedInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_dis_stage HostAssociatedInterface sample disease stage enumeration 1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. infection false samp_dis_stage_enum MIXS:0000249 sample disease stage +samp_mat_process HostAssociatedInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size HostAssociatedInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur HostAssociatedInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc HostAssociatedInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp HostAssociatedInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature sample_link HostAssociatedInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale HostAssociatedInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale HostAssociatedInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium HostAssociatedInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem HostAssociatedInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category HostAssociatedInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type HostAssociatedInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype HostAssociatedInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +size_frac HostAssociatedInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected specific_ecosystem HostAssociatedInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +temp HostAssociatedInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature JgiMgInterface jgi_mg dh_interface JGI MG -dna_seq_project JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 false string true {text} DNA seq project ID -dna_seq_project_name JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metagenomics false string true {text} DNA seq project name -dna_samp_id JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 false string true {text} DNA sample ID Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled? -dna_sample_name JgiMgInterface Give 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. JGI_pond_041618 false string true {text} DNA sample name -dna_concentration JgiMgInterface Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 2000 0 float true {float} DNA concentration in ng/ul -dna_volume JgiMgInterface Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 1000 0 float true {float} DNA volume in ul +analysis_type JgiMgInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type dna_absorb1 JgiMgInterface Recommended value is between 1 and 3. 260/280 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/280 dna_absorb2 JgiMgInterface Recommended value is between 1 and 3. 260/230 measurement of DNA sample purity 2.02 float true {float} DNA absorbance 260/230 -dna_container_id JgiMgInterface Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 false string true {text < 20 characters} DNA container label +dna_concentration JgiMgInterface Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 2000 0 float true {float} DNA concentration in ng/ul dna_cont_type JgiMgInterface Tube or plate (96-well) plate dna_cont_type_enum true DNA container type dna_cont_well JgiMgInterface Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 false ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ string true {96 well plate pos} DNA plate position -dna_sample_format JgiMgInterface Solution in which the DNA sample has been suspended Water dna_sample_format_enum true DNA sample format +dna_container_id JgiMgInterface Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 false string true {text < 20 characters} DNA container label dna_dnase JgiMgInterface Note DNase treatment is required for all RNA samples. no YesNoEnum true DNase treatment DNA -dna_organisms JgiMgInterface List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) false string true {text} DNA expected organisms -dna_collect_site JgiMgInterface Provide information on the site your DNA sample was collected from untreated pond water false string true {text} DNA collection site dna_isolate_meth JgiMgInterface Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction false string true {text} DNA isolation method -dna_seq_project_pi JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson false string true {text} DNA seq project PI dna_project_contact JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones false string true {text} DNA seq project contact -proposal_dna JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 false string true {text} DNA proposal ID -analysis_type JgiMgInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type +dna_samp_id JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 false string true {text} DNA sample ID Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't have two identifiers. How to force uniqueness? Moot because that column will be prefilled? +dna_sample_format JgiMgInterface Solution in which the DNA sample has been suspended Water dna_sample_format_enum true DNA sample format +dna_sample_name JgiMgInterface Give 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. JGI_pond_041618 false string true {text} DNA sample name +dna_seq_project JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 false string true {text} DNA seq project ID +dna_seq_project_name JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metagenomics false string true {text} DNA seq project name +dna_seq_project_pi JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson false string true {text} DNA seq project PI +dna_volume JgiMgInterface Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 1000 0 float true {float} DNA volume in ul env_package JgiMgInterface environmental package MIxS 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 mixs extension false string +proposal_dna JgiMgInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 false string true {text} DNA proposal ID sample_link JgiMgInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage JgiMtInterface jgi_mt dh_interface JGI MT -rna_seq_project JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 false string true {text} RNA seq project ID -rna_seq_project_name JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metatranscriptomics false string true {text} RNA seq project name -rna_samp_id JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 false string true {text} RNA sample ID -rna_sample_name JgiMtInterface Give 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. JGI_pond_041618 2000 0 false string true {text} RNA sample name -rna_concentration JgiMtInterface Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 1000 0 float true {float} RNA concentration in ng/ul -rna_volume JgiMtInterface Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 float true {float} RNA volume in ul +analysis_type JgiMtInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type +dnase_rna JgiMtInterface Note DNase treatment is required for all RNA samples. no dnase_rna_enum true DNase treated +env_package JgiMtInterface environmental package MIxS 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 mixs extension false string +proposal_rna JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 false string true {text} RNA proposal ID rna_absorb1 JgiMtInterface Recommended value is between 1 and 3. 260/280 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/280 rna_absorb2 JgiMtInterface Recommended value is between 1 and 3. 260/230 measurement of RNA sample purity 2.02 float true {float} RNA absorbance 260/230 -rna_container_id JgiMtInterface Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 false string true {text} RNA container label +rna_concentration JgiMtInterface Units must be in ng/uL. Enter the numerical part only. Must be calculated using a fluorometric method. Acceptable values are 0-2000. 100 1000 0 float true {float} RNA concentration in ng/ul rna_cont_type JgiMtInterface Tube or plate (96-well) plate rna_cont_type_enum true RNA container type rna_cont_well JgiMtInterface Required when 'plate' is selected for container type.|Leave blank if the sample will be shipped in a tube.|JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass validation.|For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8). B2 false ^(?!A1|A12|H1|H12)(([A-H][1-9])|([A-H]1[0-2]))$ string true {96 well plate pos} RNA plate position -rna_sample_format JgiMtInterface Solution in which the RNA sample has been suspended Water rna_sample_format_enum true RNA sample format -dnase_rna JgiMtInterface Note DNase treatment is required for all RNA samples. no dnase_rna_enum true DNase treated -rna_organisms JgiMtInterface List any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture. expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%) false string true {text} RNA expected organisms -rna_collect_site JgiMtInterface Provide information on the site your RNA sample was collected from untreated pond water false string true {text} RNA collection site +rna_container_id JgiMtInterface Must be unique across all tubes and plates, and <20 characters. All samples in a plate should have the same plate label. Pond_MT_041618 false string true {text} RNA container label rna_isolate_meth JgiMtInterface Describe the method/protocol/kit used to extract DNA/RNA. phenol/chloroform extraction false string true {text} RNA isolation method -rna_seq_project_pi JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson false string true {text} RNA seq project PI rna_project_contact JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. John Jones false string true {text} RNA seq project contact -proposal_rna JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 504000 false string true {text} RNA proposal ID -analysis_type JgiMtInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package JgiMtInterface environmental package MIxS 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 mixs extension false string +rna_samp_id JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 187654 false string true {text} RNA sample ID +rna_sample_format JgiMtInterface Solution in which the RNA sample has been suspended Water rna_sample_format_enum true RNA sample format +rna_sample_name JgiMtInterface Give 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. JGI_pond_041618 2000 0 false string true {text} RNA sample name +rna_seq_project JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. 1191234 false string true {text} RNA seq project ID +rna_seq_project_name JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. JGI Pond metatranscriptomics false string true {text} RNA seq project name +rna_seq_project_pi JgiMtInterface Do not edit these values. A template will be provided by NMDC in which these values have been pre-filled. Jane Johnson false string true {text} RNA seq project PI +rna_volume JgiMtInterface Units must be in uL. Enter the numerical part only. Value must 0-1000. Values <25 by special permission only. 25 float true {float} RNA volume in ul sample_link JgiMtInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage MiscEnvsInterface misc_envs dh_interface Misc Envs alkalinity MiscEnvsInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity +alt MiscEnvsInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude ammonium MiscEnvsInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type MiscEnvsInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type biomass MiscEnvsInterface biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000174 {text};{float} {unit} biomass bromide MiscEnvsInterface bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000176 bromide calcium MiscEnvsInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +chem_administration MiscEnvsInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chloride MiscEnvsInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride chlorophyll MiscEnvsInterface chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000177 chlorophyll +collection_date MiscEnvsInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date density MiscEnvsInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density +depth MiscEnvsInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters diether_lipids MiscEnvsInterface diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000178 {text};{float} {unit} diether lipids diss_carb_dioxide MiscEnvsInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide diss_hydrogen MiscEnvsInterface dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000179 dissolved hydrogen diss_inorg_carb MiscEnvsInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon diss_org_nitro MiscEnvsInterface dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000162 dissolved organic nitrogen diss_oxygen MiscEnvsInterface dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000119 dissolved oxygen +ecosystem MiscEnvsInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category MiscEnvsInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype MiscEnvsInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type MiscEnvsInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev MiscEnvsInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale MiscEnvsInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale MiscEnvsInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium MiscEnvsInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package MiscEnvsInterface environmental package MIxS 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 mixs extension false string +experimental_factor MiscEnvsInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +geo_loc_name MiscEnvsInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) +horizon_meth MiscEnvsInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +lat_lon MiscEnvsInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) +misc_param MiscEnvsInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter nitrate MiscEnvsInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate nitrite MiscEnvsInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite nitro MiscEnvsInterface nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000504 nitrogen org_carb MiscEnvsInterface organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000508 organic carbon +org_matter MiscEnvsInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter +org_nitro MiscEnvsInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen organism_count MiscEnvsInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp MiscEnvsInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample perturbation MiscEnvsInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation +ph MiscEnvsInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth MiscEnvsInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method +phosphate MiscEnvsInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate phosplipid_fatt_acid MiscEnvsInterface phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid potassium MiscEnvsInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pressure MiscEnvsInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure +rel_to_oxygen MiscEnvsInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity MiscEnvsInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device MiscEnvsInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method MiscEnvsInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process MiscEnvsInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size MiscEnvsInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur MiscEnvsInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration samp_store_loc MiscEnvsInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp MiscEnvsInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link MiscEnvsInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage silicate MiscEnvsInterface silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000184 silicate -sulfate MiscEnvsInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate -water_current MiscEnvsInterface water current measurement value cubic meter per second, knots 1 Measurement of magnitude and direction of flow within a fluid 10 cubic meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000203 water current size_frac MiscEnvsInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -samp_store_dur MiscEnvsInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration sodium MiscEnvsInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium +specific_ecosystem MiscEnvsInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +sulfate MiscEnvsInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate sulfide MiscEnvsInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide -collection_date MiscEnvsInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name MiscEnvsInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon MiscEnvsInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev MiscEnvsInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp MiscEnvsInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth MiscEnvsInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process MiscEnvsInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device MiscEnvsInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method MiscEnvsInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration MiscEnvsInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size MiscEnvsInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen MiscEnvsInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt MiscEnvsInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph MiscEnvsInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor MiscEnvsInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth MiscEnvsInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param MiscEnvsInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp MiscEnvsInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample temp MiscEnvsInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -ph_meth MiscEnvsInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -org_matter MiscEnvsInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter -org_nitro MiscEnvsInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen -phosphate MiscEnvsInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity MiscEnvsInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type MiscEnvsInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package MiscEnvsInterface environmental package MIxS 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 mixs extension false string -sample_link MiscEnvsInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale MiscEnvsInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale MiscEnvsInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium MiscEnvsInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem MiscEnvsInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category MiscEnvsInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type MiscEnvsInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype MiscEnvsInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem MiscEnvsInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +water_current MiscEnvsInterface water current measurement value cubic meter per second, knots 1 Measurement of magnitude and direction of flow within a fluid 10 cubic meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000203 water current PlantAssociatedInterface plant_associated dh_interface Plant Associated -organism_count PlantAssociatedInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -perturbation PlantAssociatedInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation -samp_store_loc PlantAssociatedInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +air_temp_regm PlantAssociatedInterface air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen +alt PlantAssociatedInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +analysis_type PlantAssociatedInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type ances_data PlantAssociatedInterface ancestral data free text 1 Information 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) A/3*B false string MIXS:0000247 {text} ancestral data antibiotic_regm PlantAssociatedInterface antibiotic regimen antibiotic name;antibiotic amount;treatment interval and duration milligram m Information 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 penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000553 {text};{float} {unit};{Rn/start_time/end_time/duration} antibiotic regimen biol_stat PlantAssociatedInterface biological status enumeration 1 The level of genome modification. natural false biol_stat_enum MIXS:0000858 biological status +biotic_regm PlantAssociatedInterface biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string true MIXS:0001038 {text} biotic regimen +chem_administration PlantAssociatedInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chem_mutagen PlantAssociatedInterface chemical mutagen mutagen name;mutagen amount;treatment interval and duration milligram per liter m Treatment 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 nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000555 {text};{float} {unit};{Rn/start_time/end_time/duration} chemical mutagen +climate_environment PlantAssociatedInterface Treatment 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 false string true MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example.|description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." +collection_date PlantAssociatedInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date cult_root_med PlantAssociatedInterface culture rooting medium name, PMID,DOI or url 1 Name 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. http://himedialabs.com/TD/PT158.pdf false string MIXS:0001041 {text}|{PMID}|{DOI}|{URL} culture rooting medium +depth PlantAssociatedInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters +ecosystem PlantAssociatedInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category PlantAssociatedInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype PlantAssociatedInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type PlantAssociatedInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev PlantAssociatedInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale PlantAssociatedInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale PlantAssociatedInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium PlantAssociatedInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package PlantAssociatedInterface environmental package MIxS 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 mixs extension false string +experimental_factor PlantAssociatedInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor fertilizer_regm PlantAssociatedInterface fertilizer regimen fertilizer name;fertilizer amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000556 {text};{float} {unit};{Rn/start_time/end_time/duration} fertilizer regimen fungicide_regm PlantAssociatedInterface fungicide regimen fungicide name;fungicide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000557 {text};{float} {unit};{Rn/start_time/end_time/duration} fungicide regimen +gaseous_environment PlantAssociatedInterface Use 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 CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override|would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override genetic_mod PlantAssociatedInterface genetic modification PMID,DOI,url or free text 1 Genetic 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 aox1A transgenic false string MIXS:0000859 {PMID}|{DOI}|{URL}|{text} genetic modification +geo_loc_name PlantAssociatedInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) gravity PlantAssociatedInterface gravity gravity factor value;treatment interval and duration meter per square second, g m Information 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 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000559 {float} {unit};{Rn/start_time/end_time/duration} gravity +growth_facil PlantAssociatedInterface growth facility free text or CO 1 Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Growth chamber [CO_715:0000189] false Removed from description: Alternatively use Crop Ontology (CO) terms GrowthFacilEnum true MIXS:0001043 {text}|{termLabel} {[termID]} growth facility growth_habit PlantAssociatedInterface growth habit enumeration 1 Characteristic shape, appearance or growth form of a plant species spreading false growth_habit_enum MIXS:0001044 growth habit growth_hormone_regm PlantAssociatedInterface growth hormone regimen growth hormone name;growth hormone amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000560 {text};{float} {unit};{Rn/start_time/end_time/duration} growth hormone regimen herbicide_regm PlantAssociatedInterface herbicide regimen herbicide name;herbicide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000561 {text};{float} {unit};{Rn/start_time/end_time/duration} herbicide regimen +horizon_meth PlantAssociatedInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method host_age PlantAssociatedInterface host age value year, day, hour 1 Age 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 10 days false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000255 host age host_common_name PlantAssociatedInterface host common name common name 1 Common name of the host. human false string MIXS:0000248 {text} host common name host_dry_mass PlantAssociatedInterface host dry mass measurement value kilogram, gram 1 Measurement of dry mass 500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000257 host dry mass @@ -1354,9 +1365,16 @@ host_symbiont PlantAssociatedInterface observed host symbionts species name or host_taxid PlantAssociatedInterface host taxid NCBI taxon identifier 1 NCBI taxon id of the host, e.g. 9606 7955 false string MIXS:0000250 {NCBI taxid} host taxid host_tot_mass PlantAssociatedInterface host total mass measurement value kilogram, gram 1 Total mass of the host at collection, the unit depends on host 2500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000263 host total mass host_wet_mass PlantAssociatedInterface host wet mass measurement value kilogram, gram 1 Measurement of wet mass 1500 gram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000567 host wet mass +humidity_regm PlantAssociatedInterface humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen +lat_lon PlantAssociatedInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) +light_regm PlantAssociatedInterface light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen mechanical_damage PlantAssociatedInterface mechanical damage damage type;body site m Information about any mechanical damage exerted on the plant; can include multiple damages and sites pruning;bark false string MIXS:0001052 {text};{text} mechanical damage mineral_nutr_regm PlantAssociatedInterface mineral nutrient regimen mineral nutrient name;mineral nutrient amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000570 {text};{float} {unit};{Rn/start_time/end_time/duration} mineral nutrient regimen +misc_param PlantAssociatedInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter non_min_nutr_regm PlantAssociatedInterface non-mineral nutrient regimen non-mineral nutrient name;non-mineral nutrient amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000571 {text};{float} {unit};{Rn/start_time/end_time/duration} non-mineral nutrient regimen +organism_count PlantAssociatedInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp PlantAssociatedInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample +perturbation PlantAssociatedInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation pesticide_regm PlantAssociatedInterface pesticide regimen pesticide name;pesticide amount;treatment interval and duration gram, mole per liter, milligram per liter m Information 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 pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000573 {text};{float} {unit};{Rn/start_time/end_time/duration} pesticide regimen ph_regm PlantAssociatedInterface pH regimen measurement value;treatment interval and duration m Information 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 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001056 {float};{Rn/start_time/end_time/duration} pH regimen plant_growth_med PlantAssociatedInterface plant growth medium EO or enumeration 1 Specification 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 hydroponic plant culture media [EO:0007067] false string MIXS:0001057 plant growth medium @@ -1365,6 +1383,7 @@ plant_sex PlantAssociatedInterface plant sex enumeration 1 Sex of the reprodu plant_struc PlantAssociatedInterface plant structure PO 1 Name 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. epidermis [PO:0005679] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0001060 {termLabel} {[termID]} plant structure radiation_regm PlantAssociatedInterface radiation regimen radiation type name;radiation amount;treatment interval and duration rad, gray m Information 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 gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000575 {text};{float} {unit};{Rn/start_time/end_time/duration} radiation regimen rainfall_regm PlantAssociatedInterface rainfall regimen measurement value;treatment interval and duration millimeter m Information 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 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000576 {float} {unit};{Rn/start_time/end_time/duration} rainfall regimen +rel_to_oxygen PlantAssociatedInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen root_cond PlantAssociatedInterface rooting conditions PMID,DOI,url or free text 1 Relevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container. http://himedialabs.com/TD/PT158.pdf false string MIXS:0001061 {PMID}|{DOI}|{URL}|{text} rooting conditions root_med_carbon PlantAssociatedInterface rooting medium carbon carbon source name;measurement value milligram per liter 1 Source of organic carbon in the culture rooting medium; e.g. sucrose. sucrose false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000577 {text};{float} {unit} rooting medium carbon root_med_macronutr PlantAssociatedInterface rooting medium macronutrients macronutrient name;measurement value milligram per liter 1 Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170¬†mg/L). KH2PO4;170¬†milligram per liter false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000578 {text};{float} {unit} rooting medium macronutrients @@ -1373,68 +1392,47 @@ root_med_ph PlantAssociatedInterface rooting medium pH measurement value 1 pH root_med_regl PlantAssociatedInterface rooting medium regulators regulator name;measurement value milligram per liter 1 Growth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5¬†mg/L NAA. abscisic acid;0.75 milligram per liter false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000581 {text};{float} {unit} rooting medium regulators root_med_solid PlantAssociatedInterface rooting medium solidifier name 1 Specification of the solidifying agent in the culture rooting medium; e.g. agar. agar false string MIXS:0001063 {text} rooting medium solidifier root_med_suppl PlantAssociatedInterface rooting medium organic supplements supplement name;measurement value milligram per liter 1 Organic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5¬†mg/L). nicotinic acid;0.5 milligram per liter false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string MIXS:0000580 {text};{float} {unit} rooting medium organic supplements +salinity PlantAssociatedInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity salt_regm PlantAssociatedInterface salt regimen salt name;salt amount;treatment interval and duration gram, microgram, mole per liter, gram per liter m Information 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 NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000582 {text};{float} {unit};{Rn/start_time/end_time/duration} salt regimen samp_capt_status PlantAssociatedInterface sample capture status enumeration 1 Reason for the sample farm sample false samp_capt_status_enum MIXS:0000860 sample capture status +samp_collec_device PlantAssociatedInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method PlantAssociatedInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method samp_dis_stage PlantAssociatedInterface sample disease stage enumeration 1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. infection false samp_dis_stage_enum MIXS:0000249 sample disease stage +samp_mat_process PlantAssociatedInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size PlantAssociatedInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur PlantAssociatedInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc PlantAssociatedInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp PlantAssociatedInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link PlantAssociatedInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage season_environment PlantAssociatedInterface seasonal environment seasonal environment name;treatment interval and duration m Treatment 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 rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001068 {text};{Rn/start_time/end_time/duration} seasonal environment size_frac PlantAssociatedInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +specific_ecosystem PlantAssociatedInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true standing_water_regm PlantAssociatedInterface standing water regimen standing water type;treatment interval and duration m Treatment 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 standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0001069 {text};{Rn/start_time/end_time/duration} standing water regimen +temp PlantAssociatedInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature tiss_cult_growth_med PlantAssociatedInterface tissue culture growth media PMID,DOI,url or free text 1 Description of plant tissue culture growth media used https://link.springer.com/content/pdf/10.1007/BF02796489.pdf false string MIXS:0001070 {PMID}|{DOI}|{URL}|{text} tissue culture growth media water_temp_regm PlantAssociatedInterface water temperature regimen measurement value;treatment interval and duration degree Celsius m Information 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 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string MIXS:0000590 {float} {unit};{Rn/start_time/end_time/duration} water temperature regimen -samp_store_dur PlantAssociatedInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration -growth_facil PlantAssociatedInterface growth facility free text or CO 1 Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Growth chamber [CO_715:0000189] false Removed from description: Alternatively use Crop Ontology (CO) terms GrowthFacilEnum true MIXS:0001043 {text}|{termLabel} {[termID]} growth facility -collection_date PlantAssociatedInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name PlantAssociatedInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon PlantAssociatedInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev PlantAssociatedInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp PlantAssociatedInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth PlantAssociatedInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process PlantAssociatedInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -biotic_regm PlantAssociatedInterface biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string true MIXS:0001038 {text} biotic regimen -samp_collec_device PlantAssociatedInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method PlantAssociatedInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -air_temp_regm PlantAssociatedInterface air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen -chem_administration PlantAssociatedInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size PlantAssociatedInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -climate_environment PlantAssociatedInterface Treatment 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 false string true MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example.|description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." -gaseous_environment PlantAssociatedInterface Use 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 CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override|would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override -humidity_regm PlantAssociatedInterface humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen -rel_to_oxygen PlantAssociatedInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -light_regm PlantAssociatedInterface light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen watering_regm PlantAssociatedInterface Information 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 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M|75% water holding capacity; constant false string true MIXS:0000591 {float} {unit};{Rn/start_time/end_time/duration} watering regimen -alt PlantAssociatedInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -experimental_factor PlantAssociatedInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth PlantAssociatedInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param PlantAssociatedInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp PlantAssociatedInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp PlantAssociatedInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -salinity PlantAssociatedInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type PlantAssociatedInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package PlantAssociatedInterface environmental package MIxS 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 mixs extension false string -sample_link PlantAssociatedInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale PlantAssociatedInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale PlantAssociatedInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium PlantAssociatedInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem PlantAssociatedInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category PlantAssociatedInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type PlantAssociatedInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype PlantAssociatedInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem PlantAssociatedInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true SampIdNewTermsMixin Mixin with SampIdNew Terms true SampId New Terms SampleData represents data produced by the DataHarmonizer tabs of the submission portal SampleData SedimentInterface sediment dh_interface Sediment alkalinity SedimentInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity alkyl_diethers SedimentInterface alkyl diethers measurement value mole per liter 1 Concentration of alkyl diethers 0.005 mole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000490 alkyl diethers +alt SedimentInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude aminopept_act SedimentInterface aminopeptidase activity measurement value mole per liter per hour 1 Measurement of aminopeptidase activity 0.269 mole per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000172 aminopeptidase activity ammonium SedimentInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type SedimentInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type bacteria_carb_prod SedimentInterface bacterial carbon production measurement value nanogram per hour 1 Measurement of bacterial carbon production 2.53 microgram per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000173 bacterial carbon production biomass SedimentInterface biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000174 {text};{float} {unit} biomass bishomohopanol SedimentInterface bishomohopanol measurement value microgram per liter, microgram per gram 1 Concentration of bishomohopanol 14 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000175 bishomohopanol bromide SedimentInterface bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000176 bromide calcium SedimentInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +carb_nitro_ratio SedimentInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio +chem_administration SedimentInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chloride SedimentInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride chlorophyll SedimentInterface chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000177 chlorophyll +collection_date SedimentInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date density SedimentInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density +depth SedimentInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters diether_lipids SedimentInterface diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000178 {text};{float} {unit} diether lipids diss_carb_dioxide SedimentInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide diss_hydrogen SedimentInterface dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000179 dissolved hydrogen @@ -1442,380 +1440,374 @@ diss_inorg_carb SedimentInterface dissolved inorganic carbon measurement value diss_org_carb SedimentInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon diss_org_nitro SedimentInterface dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000162 dissolved organic nitrogen diss_oxygen SedimentInterface dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000119 dissolved oxygen +ecosystem SedimentInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category SedimentInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype SedimentInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type SedimentInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true +elev SedimentInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale SedimentInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale SedimentInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium SedimentInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package SedimentInterface environmental package MIxS 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 mixs extension false string +experimental_factor SedimentInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +geo_loc_name SedimentInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) glucosidase_act SedimentInterface glucosidase activity measurement value mol per liter per hour 1 Measurement of glucosidase activity 5 mol per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000137 glucosidase activity +horizon_meth SedimentInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method +lat_lon SedimentInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) magnesium SedimentInterface magnesium measurement value mole per liter, milligram per liter, parts per million, micromole per kilogram 1 Concentration of magnesium in the sample 52.8 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000431 magnesium mean_frict_vel SedimentInterface mean friction velocity measurement value meter per second 1 Measurement of mean friction velocity 0.5 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000498 mean friction velocity mean_peak_frict_vel SedimentInterface mean peak friction velocity measurement value meter per second 1 Measurement of mean peak friction velocity 1 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000502 mean peak friction velocity methane SedimentInterface methane measurement value micromole per liter, parts per billion, parts per million 1 Methane (gas) amount or concentration at the time of sampling 1800 parts per billion false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000101 methane +misc_param SedimentInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter n_alkanes SedimentInterface n-alkanes n-alkane name;measurement value micromole per liter m Concentration of n-alkanes; can include multiple n-alkanes n-hexadecane;100 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000503 {text};{float} {unit} n-alkanes nitrate SedimentInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate nitrite SedimentInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite nitro SedimentInterface nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000504 nitrogen org_carb SedimentInterface organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000508 organic carbon +org_matter SedimentInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter +org_nitro SedimentInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen organism_count SedimentInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp SedimentInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample part_org_carb SedimentInterface particulate organic carbon measurement value microgram per liter 1 Concentration of particulate organic carbon 1.92 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000515 particulate organic carbon particle_class SedimentInterface particle classification particle name;measurement value micrometer m Particles 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 false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000206 {text};{float} {unit} particle classification perturbation SedimentInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation petroleum_hydrocarb SedimentInterface petroleum hydrocarbon measurement value micromole per liter 1 Concentration of petroleum hydrocarbon 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000516 petroleum hydrocarbon +ph SedimentInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth SedimentInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method phaeopigments SedimentInterface phaeopigments phaeopigment name;measurement value milligram per cubic meter m Concentration of phaeopigments; can include multiple phaeopigments 2.5 milligram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000180 {text};{float} {unit} phaeopigments +phosphate SedimentInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate phosplipid_fatt_acid SedimentInterface phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid porosity SedimentInterface porosity measurement value or range percentage 1 Porosity of deposited sediment is volume of voids divided by the total volume of sample false string MIXS:0000211 {float} - {float} {unit} porosity potassium SedimentInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pressure SedimentInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure redox_potential SedimentInterface redox potential measurement value millivolt 1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential 300 millivolt false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000182 redox potential +rel_to_oxygen SedimentInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity SedimentInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device SedimentInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method SedimentInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process SedimentInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size SedimentInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_dur SedimentInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration samp_store_loc SedimentInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp SedimentInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link SedimentInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage sediment_type SedimentInterface sediment type enumeration 1 Information about the sediment type based on major constituents biogenous false sediment_type_enum MIXS:0001078 sediment type silicate SedimentInterface silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000184 silicate -sulfate SedimentInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate -tidal_stage SedimentInterface tidal stage enumeration 1 Stage of tide high tide false tidal_stage_enum MIXS:0000750 tidal stage -tot_depth_water_col SedimentInterface total depth of water column measurement value meter 1 Measurement of total depth of water column 500 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000634 total depth of water column -turbidity SedimentInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity size_frac SedimentInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -samp_store_dur SedimentInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration sodium SedimentInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium +specific_ecosystem SedimentInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +sulfate SedimentInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate sulfide SedimentInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide -collection_date SedimentInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name SedimentInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon SedimentInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev SedimentInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp SedimentInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth SedimentInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process SedimentInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device SedimentInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method SedimentInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration SedimentInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size SedimentInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen SedimentInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt SedimentInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph SedimentInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor SedimentInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth SedimentInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param SedimentInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp SedimentInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample temp SedimentInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -water_content SedimentInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? -ph_meth SedimentInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -carb_nitro_ratio SedimentInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio -org_matter SedimentInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter -org_nitro SedimentInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen +tidal_stage SedimentInterface tidal stage enumeration 1 Stage of tide high tide false tidal_stage_enum MIXS:0000750 tidal stage tot_carb SedimentInterface Total carbon content 1 ug/L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000525 total carbon is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format|is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format +tot_depth_water_col SedimentInterface total depth of water column measurement value meter 1 Measurement of total depth of water column 500 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000634 total depth of water column tot_nitro_content SedimentInterface Total nitrogen content of the sample 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000530 total nitrogen content tot_org_carb SedimentInterface Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000533 total organic carbon check description. How are they different?|check description. How are they different? -phosphate SedimentInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity SedimentInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type SedimentInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package SedimentInterface environmental package MIxS 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 mixs extension false string -sample_link SedimentInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale SedimentInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale SedimentInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium SedimentInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem SedimentInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category SedimentInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type SedimentInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype SedimentInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem SedimentInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true +turbidity SedimentInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity +water_content SedimentInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? SoilInterface soil dh_interface Soil -collection_time SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} collection time, GMT -collection_date_inc SoilInterface Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was harvested/collected/ended. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation collection date -collection_time_inc SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was harvested/collected/ended. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation collection time, GMT -start_date_inc SoilInterface Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation start date -start_time_inc SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation start time, GMT -filter_method SoilInterface describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci false string true {text} filter method -experimental_factor_other SoilInterface This slot accepts open-ended text about your sample.|We recommend using key:value pairs.|Provided pairs will be considered for inclusion as future slots/terms in this data collection template. Other details about your sample that you feel can't be accurately represented in the available columns. experimental treatment: value false string true {text} experimental factor- other -non_microb_biomass SoilInterface Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string {text};{float} {unit} non-microbial biomass -non_microb_biomass_method SoilInterface "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 false string {PMID}|{DOI}|{URL} non-microbial biomass method -microbial_biomass_c SoilInterface If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass carbon -micro_biomass_c_meth SoilInterface "required if ""microbial_biomass_c"" is provided" Reference or method used in determining microbial biomass carbon https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string true {PMID}|{DOI}|{URL} microbial biomass carbon method How should we separate values? | or ;? lets be consistent -microbial_biomass_n SoilInterface If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass nitrogen -micro_biomass_n_meth SoilInterface "required if ""microbial_biomass_n"" is provided" Reference or method used in determining microbial biomass nitrogen https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string {PMID}|{DOI}|{URL} microbial biomass nitrogen method -org_nitro_method SoilInterface "required if ""org_nitro"" is provided" Method used for obtaining organic nitrogen https://doi.org/10.1016/0038-0717(85)90144-0 false string {PMID}|{DOI}|{URL} organic nitrogen method -other_treatment SoilInterface This is an open text field to provide any treatments that cannot be captured in the provided slots. Other treatments applied to your samples that are not applicable to the provided fields false string true {text} other treatments -isotope_exposure SoilInterface This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\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)?)?)?)?$ string true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? -lbc_thirty SoilInterface lbc_thirty|lbc30|lime buffer capacity (at 30 minutes) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined after 30 minute incubation 543 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string lime buffer capacity (at 30 minutes) -lbceq SoilInterface lbceq|lime buffer capacity (at 5-day equilibrium) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined at equilibrium after 5 day incubation 1575 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string lime buffer capacity (after 5 day incubation) -manganese SoilInterface manganese measurement value mg/kg (ppm) 1 Concentration of manganese in the sample 24.7 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string manganese -zinc SoilInterface zinc measurement value mg/kg (ppm) 1 Concentration of zinc in the sample 2.5 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string zinc -ammonium_nitrogen SoilInterface ammonium_nitrogen|NH4-N measurement value mg/kg 1 Concentration of ammonium nitrogen in the sample 2.3 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string ammonium nitrogen -nitrate_nitrogen SoilInterface nitrate_nitrogen|NO3-N measurement value mg/kg 1 often below some specified limit of detection Concentration of nitrate nitrogen in the sample 0.29 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string nitrate_nitrogen -nitrite_nitrogen SoilInterface nitrite_nitrogen|NO2-N measurement value mg/kg 1 Concentration of nitrite nitrogen in the sample 1.2 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string nitrite_nitrogen -growth_facil SoilInterface growth facility free text or CO 1 Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Growth chamber [CO_715:0000189] false Removed from description: Alternatively use Crop Ontology (CO) terms GrowthFacilEnum true MIXS:0001043 {text}|{termLabel} {[termID]} growth facility -store_cond SoilInterface storage conditions storage condition type;duration 1 Explain how the soil sample is stored (fresh/frozen/other). -20 degree Celsius freezer;P2Y10D false StoreCondEnum true MIXS:0000327 {text};{duration} storage conditions -collection_date SoilInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name SoilInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon SoilInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev SoilInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp SoilInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -sieving SoilInterface Describe how samples were composited or sieved.|Use 'sample link' to indicate which samples were combined. Collection design of pooled samples and/or sieve size and amount of sample sieved combined 2 cores|4mm sieved|4 mm sieved and homogenized|50 g|5 cores|2 mm sieved false string true MIXS:0000322 {{text}|{float} {unit}};{float} {unit} composite design/sieving check validation and examples|check validation and examples -depth SoilInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -size_frac_low SoilInterface size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000735 size-fraction lower threshold -size_frac_up SoilInterface size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000736 size-fraction upper threshold -samp_mat_process SoilInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -biotic_regm SoilInterface biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string true MIXS:0001038 {text} biotic regimen -samp_collec_device SoilInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method SoilInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -air_temp_regm SoilInterface air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen -chem_administration SoilInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size SoilInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -climate_environment SoilInterface Treatment 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 false string true MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example.|description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." -gaseous_environment SoilInterface Use 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 CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override|would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override -humidity_regm SoilInterface humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen -biotic_relationship SoilInterface observed biotic relationship enumeration Description 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 free living false biotic_relationship_enum MIXS:0000028 observed biotic relationship -rel_to_oxygen SoilInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -light_regm SoilInterface light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen -watering_regm SoilInterface Information 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 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M|75% water holding capacity; constant false string true MIXS:0000591 {float} {unit};{Rn/start_time/end_time/duration} watering regimen -alt SoilInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph SoilInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -slope_aspect SoilInterface Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing. The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. 35 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000647 slope aspect This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot agrochem_addition SoilInterface history/agrochemical additions agrochemical name;agrochemical amount;timestamp gram, mole per liter, milligram per liter m Addition of fertilizers, pesticides, etc. - amount and time of applications roundup;5 milligram per liter;2018-06-21 false .* string MIXS:0000639 {text};{float} {unit};{timestamp} history/agrochemical additions +air_temp_regm SoilInterface air temperature regimen temperature value;treatment interval and duration meter m Information 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 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000551 {float} {unit};{Rn/start_time/end_time/duration} air temperature regimen al_sat SoilInterface Aluminum saturation is the percentage of the CEC occupies by aluminum. Like all cations, aluminum held by the cation exchange complex is in equilibrium with aluminum in the soil solution. The relative abundance of aluminum in the sample 0.27 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000607 aluminum saturation/ extreme unusual properties This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. al_sat_meth SoilInterface Required when aluminum saturation is provided. Reference or method used in determining Aluminum saturation https://doi.org/10.1371/journal.pone.0176357 false string MIXS:0000324 {PMID}|{DOI}|{URL} aluminum saturation method/ extreme unusual properties This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I think it's weird the way GSC writes the title. I recommend this change. Thoughts?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? +alt SoilInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +ammonium_nitrogen SoilInterface ammonium_nitrogen|NH4-N measurement value mg/kg 1 Concentration of ammonium nitrogen in the sample 2.3 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string ammonium nitrogen +analysis_type SoilInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type annual_precpt SoilInterface The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. 8.94 inch false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000644 mean annual precipitation This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot|This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot annual_temp SoilInterface mean annual temperature measurement value degree Celsius 1 Mean annual temperature 12.5 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000642 mean annual temperature +biotic_regm SoilInterface biotic regimen free text 1 Information about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi. sample inoculated with Rhizobium spp. Culture false string true MIXS:0001038 {text} biotic regimen +biotic_relationship SoilInterface observed biotic relationship enumeration Description 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 free living false biotic_relationship_enum MIXS:0000028 observed biotic relationship +carb_nitro_ratio SoilInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio +chem_administration SoilInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration +climate_environment SoilInterface Treatment 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 false string true MIXS:0001040 {text};{Rn/start_time/end_time/duration} climate environment "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example.|description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." +collection_date SoilInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +collection_date_inc SoilInterface Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was harvested/collected/ended. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation collection date +collection_time SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} collection time, GMT +collection_time_inc SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was harvested/collected/ended. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation collection time, GMT crop_rotation SoilInterface history/crop rotation crop rotation status;schedule 1 Whether or not crop is rotated, and if yes, rotation schedule yes;R2/2017-01-01/2018-12-31/P6M false string MIXS:0000318 {boolean};{Rn/start_time/end_time/duration} history/crop rotation cur_land_use SoilInterface current land use enumeration 1 Present state of sample site conifers false cur_land_use_enum MIXS:0001080 current land use cur_vegetation SoilInterface Values provided here can be specific species of vegetation or vegetation regions|See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region Vegetation classification from one or more standard classification systems, or agricultural crop deciduous forest|forest|Bauhinia variegata false string MIXS:0000312 {text} current vegetation This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Recommend changing this from text value to some king of ontology?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Recommend changing this from text value to some kind of ontology? cur_vegetation_meth SoilInterface Required when current vegetation is provided. Reference or method used in vegetation classification https://doi.org/10.1111/j.1654-109X.2011.01154.x false string MIXS:0000314 {PMID}|{DOI}|{URL} current vegetation method This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided.|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided. +depth SoilInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters drainage_class SoilInterface drainage classification enumeration 1 Drainage classification from a standard system such as the USDA system well false drainage_class_enum MIXS:0001085 drainage classification +ecosystem SoilInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. EcosystemEnum true +ecosystem_category SoilInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. string or EcosystemCategoryEnum range? EcosystemCategoryEnum true +ecosystem_subtype SoilInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. string or EcosystemSubtypeEnum range? EcosystemSubtypeEnum true +ecosystem_type SoilInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. string or EcosystemTypeEnum range? EcosystemTypeEnum true +elev SoilInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters +env_broad_scale SoilInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvBroadScaleSoilEnum true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale SoilInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvLocalScaleSoilEnum true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium SoilInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvMediumSoilEnum true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package SoilInterface environmental package MIxS 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 mixs extension false string experimental_factor SoilInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +experimental_factor_other SoilInterface This slot accepts open-ended text about your sample.|We recommend using key:value pairs.|Provided pairs will be considered for inclusion as future slots/terms in this data collection template. Other details about your sample that you feel can't be accurately represented in the available columns. experimental treatment: value false string true {text} experimental factor- other extreme_event SoilInterface date, string Unusual physical events that may have affected microbial populations 1980-05-18, volcanic eruption false string MIXS:0000320 history/extreme events This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot fao_class SoilInterface soil_taxonomic/FAO classification enumeration 1 Soil 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 Luvisols false fao_class_enum MIXS:0001083 soil_taxonomic/FAO classification +filter_method SoilInterface describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci false string true {text} filter method fire SoilInterface date string Provide the date the fire occurred. If extended burning occurred provide the date range. Historical and/or physical evidence of fire 1871-10-10|1871-10-01 to 1871-10-31 false ^[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]))?)?)?$ string MIXS:0001086 history/fire "is ""to"" acceptable? Is there a better way to request that be written?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|is ""to"" acceptable? Is there a better way to request that be written?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" flooding SoilInterface date string Provide the date the flood occurred. If extended flooding occurred provide the date range. Historical and/or physical evidence of flooding 1927-04-15|1927-04 to 1927-05 false string MIXS:0000319 history/flooding "is ""to"" acceptable? Is there a better way to request that be written?|What about if the ""day"" isn't known? Is this ok?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|is ""to"" acceptable? Is there a better way to request that be written?|What about if the ""day"" isn't known? Is this ok?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" +gaseous_environment SoilInterface Use 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 CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000558 {text};{float} {unit};{Rn/start_time/end_time/duration} gaseous environment would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override|would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override +geo_loc_name SoilInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) +growth_facil SoilInterface growth facility free text or CO 1 Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Growth chamber [CO_715:0000189] false Removed from description: Alternatively use Crop Ontology (CO) terms GrowthFacilEnum true MIXS:0001043 {text}|{termLabel} {[termID]} growth facility heavy_metals SoilInterface For multiple heavy metals and concentrations, separate by ; Heavy metals present in the sample and their concentrations. mercury 0.09 micrograms per gram|mercury 0.09 ug/g; chromium 0.03 ug/g false Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal.|Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal. ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000652 {text};{float} {unit} heavy metals/ extreme unusual properties This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement.|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. heavy_metals_meth SoilInterface Required when heavy metals are provided|If different methods are used for multiple metals, indicate the metal and method. Separate metals by ; Reference or method used in determining heavy metals https://doi.org/10.3390/ijms9040434|mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8 false string MIXS:0000343 {PMID}|{DOI}|{URL} heavy metals method/ extreme unusual properties This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot horizon_meth SoilInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} soil horizon method +humidity_regm SoilInterface humidity regimen humidity value;treatment interval and duration gram per cubic meter m Information 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 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M false string true MIXS:0000568 {float} {unit};{Rn/start_time/end_time/duration} humidity regimen +isotope_exposure SoilInterface This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\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)?)?)?)?$ string true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? +lat_lon SoilInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) +lbc_thirty SoilInterface lbc_thirty|lbc30|lime buffer capacity (at 30 minutes) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined after 30 minute incubation 543 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string lime buffer capacity (at 30 minutes) +lbceq SoilInterface lbceq|lime buffer capacity (at 5-day equilibrium) measurement value ppm CaCO3/pH 1 This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one pH unit lime buffer capacity, determined at equilibrium after 5 day incubation 1575 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string lime buffer capacity (after 5 day incubation) +light_regm SoilInterface light regimen exposure type;light intensity;light quality lux; micrometer, nanometer, angstrom 1 Information about treatment(s) involving exposure to light, including both light intensity and quality. incandescant light;10 lux;450 nanometer false ^\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string true MIXS:0000569 {text};{float} {unit};{float} {unit} light regimen link_class_info SoilInterface link to classification information PMID,DOI or url 1 Link to digitized soil maps or other soil classification information false string MIXS:0000329 {PMID}|{DOI}|{URL} link to classification information link_climate_info SoilInterface link to climate information PMID,DOI or url 1 Link to climate resource false string MIXS:0000328 {PMID}|{DOI}|{URL} link to climate information local_class SoilInterface soil_taxonomic/local classification local classification name 1 Soil classification based on local soil classification system false string MIXS:0000330 {text} soil_taxonomic/local classification -misc_param SoilInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter local_class_meth SoilInterface soil_taxonomic/local classification method PMID,DOI or url 1 Reference or method used in determining the local soil classification false string MIXS:0000331 {PMID}|{DOI}|{URL} soil_taxonomic/local classification method +manganese SoilInterface manganese measurement value mg/kg (ppm) 1 Concentration of manganese in the sample 24.7 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string manganese +micro_biomass_c_meth SoilInterface "required if ""microbial_biomass_c"" is provided" Reference or method used in determining microbial biomass carbon https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string true {PMID}|{DOI}|{URL} microbial biomass carbon method How should we separate values? | or ;? lets be consistent +micro_biomass_meth SoilInterface microbial biomass method PMID,DOI or url 1 Reference or method used in determining microbial biomass false string MIXS:0000339 {PMID}|{DOI}|{URL} microbial biomass method +micro_biomass_n_meth SoilInterface "required if ""microbial_biomass_n"" is provided" Reference or method used in determining microbial biomass nitrogen https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string {PMID}|{DOI}|{URL} microbial biomass nitrogen method +microbial_biomass SoilInterface microbial biomass measurement value ton, kilogram, gram per kilogram soil 1 The 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 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000650 microbial biomass +microbial_biomass_c SoilInterface If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass carbon +microbial_biomass_n SoilInterface If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass nitrogen +misc_param SoilInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +nitrate_nitrogen SoilInterface nitrate_nitrogen|NO3-N measurement value mg/kg 1 often below some specified limit of detection Concentration of nitrate nitrogen in the sample 0.29 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string nitrate_nitrogen +nitrite_nitrogen SoilInterface nitrite_nitrogen|NO2-N measurement value mg/kg 1 Concentration of nitrite nitrogen in the sample 1.2 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string nitrite_nitrogen +non_microb_biomass SoilInterface Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string {text};{float} {unit} non-microbial biomass +non_microb_biomass_method SoilInterface "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 false string {PMID}|{DOI}|{URL} non-microbial biomass method +org_matter SoilInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter +org_nitro SoilInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen +org_nitro_method SoilInterface "required if ""org_nitro"" is provided" Method used for obtaining organic nitrogen https://doi.org/10.1016/0038-0717(85)90144-0 false string {PMID}|{DOI}|{URL} organic nitrogen method +other_treatment SoilInterface This is an open text field to provide any treatments that cannot be captured in the provided slots. Other treatments applied to your samples that are not applicable to the provided fields false string true {text} other treatments oxy_stat_samp SoilInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample +ph SoilInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth SoilInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method +phosphate SoilInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate prev_land_use_meth SoilInterface history/previous land use method PMID,DOI or url 1 Reference or method used in determining previous land use and dates false string MIXS:0000316 {PMID}|{DOI}|{URL} history/previous land use method previous_land_use SoilInterface history/previous land use land use name;date 1 Previous land use and dates false ^\S+.*\S+;([\+-]?\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)?)?)?)?$ string MIXS:0000315 {text};{timestamp} history/previous land use profile_position SoilInterface profile position enumeration 1 Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas summit false profile_position_enum MIXS:0001084 profile position +rel_to_oxygen SoilInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity SoilInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +salinity_meth SoilInterface Reference or method used in determining salinity https://doi.org/10.1007/978-1-61779-986-0_28 false string MIXS:0000341 {PMID}|{DOI}|{URL} salinity method +samp_collec_device SoilInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method SoilInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process SoilInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size SoilInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected +samp_store_temp SoilInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link SoilInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage season_precpt SoilInterface Seasons are defined as spring (March, April, May), summer (June, July, August), autumn (September, October, November) and winter (December, January, February). The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps. 0.4 inch|10.16 mm false mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average|mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000645 average seasonal precipitation This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|check validation & examples. always mm? so value only? Or value + unit|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|check validation & examples. always mm? so value only? Or value + unit season_temp SoilInterface mean seasonal temperature measurement value degree Celsius 1 Mean seasonal temperature 18 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000643 mean seasonal temperature +sieving SoilInterface Describe how samples were composited or sieved.|Use 'sample link' to indicate which samples were combined. Collection design of pooled samples and/or sieve size and amount of sample sieved combined 2 cores|4mm sieved|4 mm sieved and homogenized|50 g|5 cores|2 mm sieved false string true MIXS:0000322 {{text}|{float} {unit}};{float} {unit} composite design/sieving check validation and examples|check validation and examples +size_frac_low SoilInterface size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000735 size-fraction lower threshold +size_frac_up SoilInterface size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000736 size-fraction upper threshold +slope_aspect SoilInterface Aspect is the orientation of slope, measured clockwise in degrees from 0 to 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270 is west-facing. The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. 35 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000647 slope aspect This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot slope_gradient SoilInterface Commonly 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 10%|10 %|0.1 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000646 slope gradient Slope is a percent. How does the validation work? Check to correct examples|Slope is a percent. How does the validation work? Check to correct examples soil_horizon SoilInterface soil horizon enumeration 1 Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath A horizon false soil_horizon_enum MIXS:0001082 soil horizon soil_text_measure SoilInterface soil texture measurement measurement value 1 The 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. false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000335 soil texture measurement soil_texture_meth SoilInterface soil texture method PMID,DOI or url 1 Reference or method used in determining soil texture false string MIXS:0000336 {PMID}|{DOI}|{URL} soil texture method soil_type SoilInterface soil type ENVO_00001998 1 Description 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. plinthosol [ENVO:00002250] false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string MIXS:0000332 {termLabel} {[termID]} soil type soil_type_meth SoilInterface soil type method PMID,DOI or url 1 Reference or method used in determining soil series name or other lower-level classification false string MIXS:0000334 {PMID}|{DOI}|{URL} soil type method +specific_ecosystem SoilInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. string or SpecificEcosystemEnum range? SpecificEcosystemEnum true +start_date_inc SoilInterface Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation start date +start_time_inc SoilInterface Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation start time, GMT +store_cond SoilInterface storage conditions storage condition type;duration 1 Explain how the soil sample is stored (fresh/frozen/other). -20 degree Celsius freezer;P2Y10D false StoreCondEnum true MIXS:0000327 {text};{duration} storage conditions temp SoilInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature tillage SoilInterface history/tillage enumeration m Note method(s) used for tilling chisel true tillage_enum MIXS:0001081 history/tillage -water_content SoilInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? -water_cont_soil_meth SoilInterface Required if providing water content Reference or method used in determining the water content of soil J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503|https://dec.alaska.gov/applications/spar/webcalc/definitions.htm false string MIXS:0000323 {PMID}|{DOI}|{URL} water content method Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this?|Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this? -ph_meth SoilInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -microbial_biomass SoilInterface microbial biomass measurement value ton, kilogram, gram per kilogram soil 1 The 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 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000650 microbial biomass -micro_biomass_meth SoilInterface microbial biomass method PMID,DOI or url 1 Reference or method used in determining microbial biomass false string MIXS:0000339 {PMID}|{DOI}|{URL} microbial biomass method -carb_nitro_ratio SoilInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio -org_matter SoilInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter -org_nitro SoilInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen tot_carb SoilInterface Total carbon content 1 ug/L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000525 total carbon is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format|is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format -tot_nitro_content SoilInterface Total nitrogen content of the sample 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000530 total nitrogen content tot_nitro_cont_meth SoilInterface Reference or method used in determining the total nitrogen https://doi.org/10.2134/agronmonogr9.2.c32|https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo false string MIXS:0000338 {PMID}|{DOI}|{URL} total nitrogen content method -tot_org_carb SoilInterface Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000533 total organic carbon check description. How are they different?|check description. How are they different? +tot_nitro_content SoilInterface Total nitrogen content of the sample 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000530 total nitrogen content tot_org_c_meth SoilInterface Reference or method used in determining total organic carbon https://doi.org/10.1080/07352680902776556 false string MIXS:0000337 {PMID}|{DOI}|{URL} total organic carbon method +tot_org_carb SoilInterface Definition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content 5 mg N/ L false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000533 total organic carbon check description. How are they different?|check description. How are they different? tot_phosp SoilInterface total phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus 0.03 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000117 total phosphorus -phosphate SoilInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity SoilInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -salinity_meth SoilInterface Reference or method used in determining salinity https://doi.org/10.1007/978-1-61779-986-0_28 false string MIXS:0000341 {PMID}|{DOI}|{URL} salinity method -analysis_type SoilInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package SoilInterface environmental package MIxS 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 mixs extension false string -sample_link SoilInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale SoilInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvBroadScaleSoilEnum true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale SoilInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvLocalScaleSoilEnum true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium SoilInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ EnvMediumSoilEnum true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem SoilInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. EcosystemEnum true -ecosystem_category SoilInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. string or EcosystemCategoryEnum range? EcosystemCategoryEnum true -ecosystem_type SoilInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. string or EcosystemTypeEnum range? EcosystemTypeEnum true -ecosystem_subtype SoilInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. string or EcosystemSubtypeEnum range? EcosystemSubtypeEnum true -specific_ecosystem SoilInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. string or SpecificEcosystemEnum range? SpecificEcosystemEnum true +water_cont_soil_meth SoilInterface Required if providing water content Reference or method used in determining the water content of soil J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503|https://dec.alaska.gov/applications/spar/webcalc/definitions.htm false string MIXS:0000323 {PMID}|{DOI}|{URL} water content method Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this?|Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this? +water_content SoilInterface string gram per gram or cubic centimeter per cubic centimeter Water content measurement 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string MIXS:0000185 water content value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods?|value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? +watering_regm SoilInterface Information 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 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M|75% water holding capacity; constant false string true MIXS:0000591 {float} {unit};{Rn/start_time/end_time/duration} watering regimen +zinc SoilInterface zinc measurement value mg/kg (ppm) 1 Concentration of zinc in the sample 2.5 mg/kg false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string zinc organism_count SoilInterface false ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other))$ string SoilMixsInspiredMixin Mixin with SoilMixsInspired Terms true Soil MIxS Inspired Mixin -collection_time SoilMixsInspiredMixin Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} collection time, GMT collection_date_inc SoilMixsInspiredMixin Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was harvested/collected/ended. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation collection date +collection_time SoilMixsInspiredMixin Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter The time of sampling, either as an instance (single point) or interval. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} collection time, GMT collection_time_inc SoilMixsInspiredMixin Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was harvested/collected/ended. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation collection time, GMT -start_date_inc SoilMixsInspiredMixin Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation start date -start_time_inc SoilMixsInspiredMixin Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation start time, GMT -filter_method SoilMixsInspiredMixin describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci false string true {text} filter method experimental_factor_other SoilMixsInspiredMixin This slot accepts open-ended text about your sample.|We recommend using key:value pairs.|Provided pairs will be considered for inclusion as future slots/terms in this data collection template. Other details about your sample that you feel can't be accurately represented in the available columns. experimental treatment: value false string true {text} experimental factor- other -non_microb_biomass SoilMixsInspiredMixin Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string {text};{float} {unit} non-microbial biomass -non_microb_biomass_method SoilMixsInspiredMixin "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 false string {PMID}|{DOI}|{URL} non-microbial biomass method -microbial_biomass_c SoilMixsInspiredMixin If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass carbon +filter_method SoilMixsInspiredMixin describe the filter or provide a catalog number and manufacturer Type of filter used or how the sample was filtered C18|Basix PES, 13-100-106 FisherSci false string true {text} filter method +isotope_exposure SoilMixsInspiredMixin This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\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)?)?)?)?$ string true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? micro_biomass_c_meth SoilMixsInspiredMixin "required if ""microbial_biomass_c"" is provided" Reference or method used in determining microbial biomass carbon https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string true {PMID}|{DOI}|{URL} microbial biomass carbon method How should we separate values? | or ;? lets be consistent -microbial_biomass_n SoilMixsInspiredMixin If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass nitrogen micro_biomass_n_meth SoilMixsInspiredMixin "required if ""microbial_biomass_n"" is provided" Reference or method used in determining microbial biomass nitrogen https://doi.org/10.1016/0038-0717(87)90052-6|https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526 false string {PMID}|{DOI}|{URL} microbial biomass nitrogen method +microbial_biomass_c SoilMixsInspiredMixin If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug C/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass carbon +microbial_biomass_n SoilMixsInspiredMixin If you provide this, correction factors used for conversion to the final units and method are required The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. 0.05 ug N/g dry soil false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string {float} {unit} microbial biomass nitrogen +non_microb_biomass SoilMixsInspiredMixin Amount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ; insect 0.23 ug; plant 1g false ^[^;\t\r\x0A\|]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A\|]+$ string {text};{float} {unit} non-microbial biomass +non_microb_biomass_method SoilMixsInspiredMixin "required if ""non-microbial biomass"" is provided" Reference or method used in determining biomass https://doi.org/10.1038/s41467-021-26181-3 false string {PMID}|{DOI}|{URL} non-microbial biomass method org_nitro_method SoilMixsInspiredMixin "required if ""org_nitro"" is provided" Method used for obtaining organic nitrogen https://doi.org/10.1016/0038-0717(85)90144-0 false string {PMID}|{DOI}|{URL} organic nitrogen method other_treatment SoilMixsInspiredMixin This is an open text field to provide any treatments that cannot be captured in the provided slots. Other treatments applied to your samples that are not applicable to the provided fields false string true {text} other treatments -isotope_exposure SoilMixsInspiredMixin This is required when your experimental design includes the use of isotopically labeled compounds List isotope exposure or addition applied to your sample. 13C glucose|H218O false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]; ([\+-]?\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)?)?)?)?$ string true {termLabel} {[termID]}; {timestamp} isotope exposure/addition Can we make the H218O correctly super and subscripted? +start_date_inc SoilMixsInspiredMixin Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are all acceptable. Date the incubation was started. Only relevant for incubation samples. 2021-04-15, 2021-04 and 2021 are all acceptable. false MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision date only string true {date, arbitrary precision} incubation start date +start_time_inc SoilMixsInspiredMixin Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter Time the incubation was started. Only relevant for incubation samples. 13:33 or 13:33:55 false MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time only string true {time, seconds optional} incubation start time, GMT WastewaterSludgeInterface wastewater_sludge dh_interface Wastewater Sludge alkalinity WastewaterSludgeInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity -nitrate WastewaterSludgeInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate -organism_count WastewaterSludgeInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count -perturbation WastewaterSludgeInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation -samp_store_loc WastewaterSludgeInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location -size_frac WastewaterSludgeInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +alt WastewaterSludgeInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude +analysis_type WastewaterSludgeInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type biochem_oxygen_dem WastewaterSludgeInterface biochemical oxygen demand measurement value milligram per liter 1 Amount 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 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000653 biochemical oxygen demand +chem_administration WastewaterSludgeInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chem_oxygen_dem WastewaterSludgeInterface chemical oxygen demand measurement value milligram per liter 1 A 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 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000656 chemical oxygen demand +collection_date WastewaterSludgeInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +depth WastewaterSludgeInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters +ecosystem WastewaterSludgeInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true +ecosystem_category WastewaterSludgeInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true +ecosystem_subtype WastewaterSludgeInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true +ecosystem_type WastewaterSludgeInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true efficiency_percent WastewaterSludgeInterface efficiency percent measurement value micromole per liter 1 Percentage of volatile solids removed from the anaerobic digestor false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000657 efficiency percent +elev WastewaterSludgeInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters emulsions WastewaterSludgeInterface emulsions emulsion name;measurement value gram per liter m Amount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000660 {text};{float} {unit} emulsions +env_broad_scale WastewaterSludgeInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale WastewaterSludgeInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium WastewaterSludgeInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package WastewaterSludgeInterface environmental package MIxS 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 mixs extension false string +experimental_factor WastewaterSludgeInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor gaseous_substances WastewaterSludgeInterface gaseous substances gaseous substance name;measurement value micromole per liter m Amount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000661 {text};{float} {unit} gaseous substances +geo_loc_name WastewaterSludgeInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) +horizon_meth WastewaterSludgeInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method indust_eff_percent WastewaterSludgeInterface industrial effluent percent measurement value percentage 1 Percentage of industrial effluents received by wastewater treatment plant false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000662 industrial effluent percent inorg_particles WastewaterSludgeInterface inorganic particles inorganic particle name;measurement value mole per liter, milligram per liter m Concentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000664 {text};{float} {unit} inorganic particles +lat_lon WastewaterSludgeInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) +misc_param WastewaterSludgeInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter +nitrate WastewaterSludgeInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate org_particles WastewaterSludgeInterface organic particles particle name;measurement value gram per liter m Concentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc. false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000665 {text};{float} {unit} organic particles +organism_count WastewaterSludgeInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^([-+]?[0-9]*\.?[0-9]+ +\S.*\|)*([-+]?[0-9]*\.?[0-9]+ +\S.*)$ string MIXS:0000103 organism count +oxy_stat_samp WastewaterSludgeInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample +perturbation WastewaterSludgeInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation +ph WastewaterSludgeInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH +ph_meth WastewaterSludgeInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method +phosphate WastewaterSludgeInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate pre_treatment WastewaterSludgeInterface pre-treatment pre-treatment type 1 The process of pre-treatment removes materials that can be easily collected from the raw wastewater false string MIXS:0000348 {text} pre-treatment primary_treatment WastewaterSludgeInterface primary treatment primary treatment type 1 The process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed false string MIXS:0000349 {text} primary treatment reactor_type WastewaterSludgeInterface reactor type reactor type name 1 Anaerobic 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 false string MIXS:0000350 {text} reactor type +rel_to_oxygen WastewaterSludgeInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity WastewaterSludgeInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device WastewaterSludgeInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method WastewaterSludgeInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process WastewaterSludgeInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size WastewaterSludgeInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected samp_store_dur WastewaterSludgeInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration +samp_store_loc WastewaterSludgeInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp WastewaterSludgeInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature +sample_link WastewaterSludgeInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage secondary_treatment WastewaterSludgeInterface secondary treatment secondary treatment type 1 The process for substantially degrading the biological content of the sewage false string MIXS:0000351 {text} secondary treatment sewage_type WastewaterSludgeInterface sewage type sewage type name 1 Type of wastewater treatment plant as municipial or industrial false string MIXS:0000215 {text} sewage type +size_frac WastewaterSludgeInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected sludge_retent_time WastewaterSludgeInterface sludge retention time measurement value hours 1 The time activated sludge remains in reactor false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000669 sludge retention time sodium WastewaterSludgeInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium soluble_inorg_mat WastewaterSludgeInterface soluble inorganic material soluble inorganic material name;measurement value gram, microgram, mole per liter, gram per liter, parts per million m Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc. false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000672 {text};{float} {unit} soluble inorganic material soluble_org_mat WastewaterSludgeInterface soluble organic material soluble organic material name;measurement value gram, microgram, mole per liter, gram per liter, parts per million m Concentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc. false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000673 {text};{float} {unit} soluble organic material +specific_ecosystem WastewaterSludgeInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true suspend_solids WastewaterSludgeInterface suspended solids suspended solid name;measurement value gram, microgram, milligram per liter, mole per liter, gram per liter, part per million m Concentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000150 {text};{float} {unit} suspended solids +temp WastewaterSludgeInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature tertiary_treatment WastewaterSludgeInterface tertiary treatment tertiary treatment type 1 The process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment false string MIXS:0000352 {text} tertiary treatment tot_nitro WastewaterSludgeInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration tot_phosphate WastewaterSludgeInterface total phosphate measurement value microgram per liter, micromole per liter 1 Total amount or concentration of phosphate false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000689 total phosphate wastewater_type WastewaterSludgeInterface wastewater type wastewater type name 1 The origin of wastewater such as human waste, rainfall, storm drains, etc. false string MIXS:0000353 {text} wastewater type -collection_date WastewaterSludgeInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name WastewaterSludgeInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {text}: {text}, {text} geographic location (country and/or sea,region) -lat_lon WastewaterSludgeInterface This is currently a required field but it's not clear if this should be required for human hosts false required where?|This is currently a required field but it's not clear if this should be required for human hosts ^[-+]?([1-8]?\d(\.\d+)?|90(\.0+)?)\s[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?)$ string MIXS:0000009 {lat lon} geographic location (latitude and longitude) -elev WastewaterSludgeInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 225|0|1250 false float true MIXS:0000093 elevation, meters -samp_store_temp WastewaterSludgeInterface sample storage temperature measurement value degree Celsius 1 Temperature at which the sample was stored (degrees are assumed) -80 Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000110 sample storage temperature -depth WastewaterSludgeInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -samp_mat_process WastewaterSludgeInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device WastewaterSludgeInterface sample collection device device name Report dimensions and details when applicable The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string true MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method WastewaterSludgeInterface sample collection method PMID,DOI,url , or text This can be a citation or description The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration WastewaterSludgeInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size WastewaterSludgeInterface amount or size of sample collected measurement value millliter, gram, milligram, liter This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 grams|10 mL false ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+$ string MIXS:0000001 {float} {unit} amount or size of sample collected -rel_to_oxygen WastewaterSludgeInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt WastewaterSludgeInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string true MIXS:0000094 altitude -ph WastewaterSludgeInterface pH measurement value 1 pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 14 0 false Use modified term float true MIXS:0001001 {float} pH -experimental_factor WastewaterSludgeInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:EFO_0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth WastewaterSludgeInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} horizon method -misc_param WastewaterSludgeInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp WastewaterSludgeInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp WastewaterSludgeInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -ph_meth WastewaterSludgeInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -phosphate WastewaterSludgeInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity WastewaterSludgeInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type WastewaterSludgeInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package WastewaterSludgeInterface environmental package MIxS 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 mixs extension false string -sample_link WastewaterSludgeInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale WastewaterSludgeInterface In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale WastewaterSludgeInterface Report the entity or entities which are in the sample or specimen’s 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. canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium WastewaterSludgeInterface Report 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). soil [ENVO:00001998] false "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem WastewaterSludgeInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. string true -ecosystem_category WastewaterSludgeInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string or EcosystemCategoryEnum range? string true -ecosystem_type WastewaterSludgeInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string or EcosystemTypeEnum range? string true -ecosystem_subtype WastewaterSludgeInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string or EcosystemSubtypeEnum range? string true -specific_ecosystem WastewaterSludgeInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string or SpecificEcosystemEnum range? string true WaterInterface water dh_interface Water alkalinity WaterInterface alkalinity measurement value milliequivalent per liter, milligram per liter 1 Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate 50 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000421 alkalinity +alkalinity_method WaterInterface alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method alkyl_diethers WaterInterface alkyl diethers measurement value mole per liter 1 Concentration of alkyl diethers 0.005 mole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000490 alkyl diethers +alt WaterInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000094 altitude aminopept_act WaterInterface aminopeptidase activity measurement value mole per liter per hour 1 Measurement of aminopeptidase activity 0.269 mole per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000172 aminopeptidase activity ammonium WaterInterface ammonium measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of ammonium in the sample 1.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000427 ammonium +analysis_type WaterInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type +atmospheric_data WaterInterface atmospheric data atmospheric data name;measurement value m Measurement of atmospheric data; can include multiple data wind speed;9 knots false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0001097 {text};{float} {unit} atmospheric data +bac_prod WaterInterface bacterial production measurement value milligram per cubic meter per day 1 Bacterial production in the water column measured by isotope uptake 5 milligram per cubic meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000683 bacterial production +bac_resp WaterInterface bacterial respiration measurement value milligram per cubic meter per day, micromole oxygen per liter per hour 1 Measurement of bacterial respiration in the water column 300 micromole oxygen per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000684 bacterial respiration bacteria_carb_prod WaterInterface bacterial carbon production measurement value nanogram per hour 1 Measurement of bacterial carbon production 2.53 microgram per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000173 bacterial carbon production biomass WaterInterface biomass biomass type;measurement value ton, kilogram, gram m Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements total;20 gram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000174 {text};{float} {unit} biomass bishomohopanol WaterInterface bishomohopanol measurement value microgram per liter, microgram per gram 1 Concentration of bishomohopanol 14 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000175 bishomohopanol bromide WaterInterface bromide measurement value parts per million 1 Concentration of bromide 0.05 parts per million false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000176 bromide calcium WaterInterface calcium measurement value milligram per liter, micromole per liter, parts per million 1 Concentration of calcium in the sample 0.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000432 calcium +carb_nitro_ratio WaterInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio +chem_administration WaterInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration chloride WaterInterface chloride measurement value milligram per liter, parts per million 1 Concentration of chloride in the sample 5000 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000429 chloride chlorophyll WaterInterface chlorophyll measurement value milligram per cubic meter, microgram per liter 1 Concentration of chlorophyll 5 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000177 chlorophyll +collection_date WaterInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date +conduc WaterInterface conductivity measurement value milliSiemens per centimeter 1 Electrical conductivity of water 10 milliSiemens per centimeter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000692 conductivity density WaterInterface density measurement value gram per cubic meter, gram per cubic centimeter 1 Density of the sample, which is its mass per unit volume (aka volumetric mass density) 1000 kilogram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000435 density +depth WaterInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters diether_lipids WaterInterface diether lipids diether lipid name;measurement value nanogram per liter m Concentration of diether lipids; can include multiple types of diether lipids 0.2 nanogram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000178 {text};{float} {unit} diether lipids diss_carb_dioxide WaterInterface dissolved carbon dioxide measurement value micromole per liter, milligram per liter 1 Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample 5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000436 dissolved carbon dioxide diss_hydrogen WaterInterface dissolved hydrogen measurement value micromole per liter 1 Concentration of dissolved hydrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000179 dissolved hydrogen diss_inorg_carb WaterInterface dissolved inorganic carbon measurement value microgram per liter, milligram per liter, parts per million 1 Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter 2059 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000434 dissolved inorganic carbon +diss_inorg_nitro WaterInterface dissolved inorganic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of dissolved inorganic nitrogen 761 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000698 dissolved inorganic nitrogen +diss_inorg_phosp WaterInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus diss_org_carb WaterInterface dissolved organic carbon measurement value micromole per liter, milligram per liter 1 Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid 197 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000433 dissolved organic carbon diss_org_nitro WaterInterface dissolved organic nitrogen measurement value microgram per liter, milligram per liter 1 Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000162 dissolved organic nitrogen diss_oxygen WaterInterface dissolved oxygen measurement value micromole per kilogram, milligram per liter 1 Concentration of dissolved oxygen 175 micromole per kilogram false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000119 dissolved oxygen +down_par WaterInterface downward PAR measurement value microEinstein per square meter per second, microEinstein per square centimeter per second 1 Visible waveband radiance and irradiance measurements in the water column 28.71 microEinstein per square meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000703 downward PAR +ecosystem WaterInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false string true +ecosystem_category WaterInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string true +ecosystem_subtype WaterInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string true +ecosystem_type WaterInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string true +elev WaterInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 100 false float MIXS:0000093 elevation, meters +env_broad_scale WaterInterface Report 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’s 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 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context +env_local_scale WaterInterface Report the entity or entities which are in the sample or specimen’s 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. false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context +env_medium WaterInterface Report 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). false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium +env_package WaterInterface environmental package MIxS 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 mixs extension false string +experimental_factor WaterInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor +fluor WaterInterface fluorescence measurement value milligram chlorophyll a per cubic meter, volts 1 Raw or converted fluorescence of water 2.5 volts false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000704 fluorescence +geo_loc_name WaterInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {term}: {term}, {text} geographic location (country and/or sea,region) glucosidase_act WaterInterface glucosidase activity measurement value mol per liter per hour 1 Measurement of glucosidase activity 5 mol per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000137 glucosidase activity +horizon_meth WaterInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} soil horizon method +lat_lon WaterInterface This is currently a required field but it's not clear if this should be required for human hosts false required where? ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string MIXS:0000009 {float} {float} geographic location (latitude and longitude) +light_intensity WaterInterface light intensity measurement value lux 1 Measurement of light intensity 0.3 lux false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000706 light intensity mean_frict_vel WaterInterface mean friction velocity measurement value meter per second 1 Measurement of mean friction velocity 0.5 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000498 mean friction velocity mean_peak_frict_vel WaterInterface mean peak friction velocity measurement value meter per second 1 Measurement of mean peak friction velocity 1 meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000502 mean peak friction velocity +misc_param WaterInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter n_alkanes WaterInterface n-alkanes n-alkane name;measurement value micromole per liter m Concentration of n-alkanes; can include multiple n-alkanes n-hexadecane;100 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000503 {text};{float} {unit} n-alkanes nitrate WaterInterface nitrate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrate in the sample 65 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000425 nitrate nitrite WaterInterface nitrite measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of nitrite in the sample 0.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000426 nitrite nitro WaterInterface nitrogen measurement value micromole per liter 1 Concentration of nitrogen (total) 4.2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000504 nitrogen org_carb WaterInterface organic carbon measurement value micromole per liter 1 Concentration of organic carbon 1.5 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000508 organic carbon +org_matter WaterInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter +org_nitro WaterInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen organism_count WaterInterface organism count organism name;measurement value;enumeration number of cells per cubic meter, number of cells per milliliter, number of cells per cubic centimeter m Total 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) total prokaryotes;3.5e7 cells per milliliter;qPCR false ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other))$ string MIXS:0000103 organism count +oxy_stat_samp WaterInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample part_org_carb WaterInterface particulate organic carbon measurement value microgram per liter 1 Concentration of particulate organic carbon 1.92 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000515 particulate organic carbon +part_org_nitro WaterInterface particulate organic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of particulate organic nitrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000719 particulate organic nitrogen perturbation WaterInterface perturbation perturbation type name;perturbation interval and duration m Type 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 antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M false string MIXS:0000754 {text};{Rn/start_time/end_time/duration} perturbation petroleum_hydrocarb WaterInterface petroleum hydrocarbon measurement value micromole per liter 1 Concentration of petroleum hydrocarbon 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000516 petroleum hydrocarbon +ph WaterInterface pH measurement value 1 Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 false double MIXS:0001001 pH +ph_meth WaterInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method phaeopigments WaterInterface phaeopigments phaeopigment name;measurement value milligram per cubic meter m Concentration of phaeopigments; can include multiple phaeopigments 2.5 milligram per cubic meter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000180 {text};{float} {unit} phaeopigments +phosphate WaterInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate phosplipid_fatt_acid WaterInterface phospholipid fatty acid phospholipid fatty acid name;measurement value mole per gram, mole per liter m Concentration of phospholipid fatty acids; can include multiple values 2.98 milligram per liter false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000181 {text};{float} {unit} phospholipid fatty acid +photon_flux WaterInterface photon flux measurement value number of photons per second per unit area 1 Measurement of photon flux 3.926 micromole photons per second per square meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000725 photon flux potassium WaterInterface potassium measurement value milligram per liter, parts per million 1 Concentration of potassium in the sample 463 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000430 potassium pressure WaterInterface pressure measurement value atmosphere 1 Pressure to which the sample is subject to, in atmospheres 50 atmosphere false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000412 pressure +primary_prod WaterInterface primary production measurement value milligram per cubic meter per day, gram per square meter per day 1 Measurement of primary production, generally measured as isotope uptake 100 milligram per cubic meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000728 primary production redox_potential WaterInterface redox potential measurement value millivolt 1 Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential 300 millivolt false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000182 redox potential +rel_to_oxygen WaterInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen +salinity WaterInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity +samp_collec_device WaterInterface sample collection device device name The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device +samp_collec_method WaterInterface sample collection method PMID,DOI,url , or text The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method +samp_mat_process WaterInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing +samp_size WaterInterface amount or size of sample collected measurement value millliter, gram, milligram, liter The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000001 amount or size of sample collected +samp_store_dur WaterInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration samp_store_loc WaterInterface sample storage location location name 1 Location at which sample was stored, usually name of a specific freezer/room Freezer no:5 false string MIXS:0000755 {text} sample storage location +samp_store_temp WaterInterface sample storage temperature measurement value degree Celsius 1 Temperature at which sample was stored, e.g. -80 degree Celsius -80 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000110 sample storage temperature +sample_link WaterInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage silicate WaterInterface silicate measurement value micromole per liter 1 Concentration of silicate 0.05 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000184 silicate +size_frac WaterInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected +size_frac_low WaterInterface size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000735 size-fraction lower threshold +size_frac_up WaterInterface size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000736 size-fraction upper threshold +sodium WaterInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium +soluble_react_phosp WaterInterface soluble reactive phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of soluble reactive phosphorus 0.1 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000738 soluble reactive phosphorus +specific_ecosystem WaterInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string true sulfate WaterInterface sulfate measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfate in the sample 5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000423 sulfate +sulfide WaterInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide +suspend_part_matter WaterInterface suspended particulate matter measurement value milligram per liter 1 Concentration of suspended particulate matter 0.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000741 suspended particulate matter +temp WaterInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature tidal_stage WaterInterface tidal stage enumeration 1 Stage of tide high tide false tidal_stage_enum MIXS:0000750 tidal stage tot_depth_water_col WaterInterface total depth of water column measurement value meter 1 Measurement of total depth of water column 500 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000634 total depth of water column -turbidity WaterInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity -alkalinity_method WaterInterface alkalinity method description of method 1 Method used for alkalinity measurement titration false string MIXS:0000298 {text} alkalinity method -atmospheric_data WaterInterface atmospheric data atmospheric data name;measurement value m Measurement of atmospheric data; can include multiple data wind speed;9 knots false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0001097 {text};{float} {unit} atmospheric data -bac_prod WaterInterface bacterial production measurement value milligram per cubic meter per day 1 Bacterial production in the water column measured by isotope uptake 5 milligram per cubic meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000683 bacterial production -bac_resp WaterInterface bacterial respiration measurement value milligram per cubic meter per day, micromole oxygen per liter per hour 1 Measurement of bacterial respiration in the water column 300 micromole oxygen per liter per hour false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000684 bacterial respiration -conduc WaterInterface conductivity measurement value milliSiemens per centimeter 1 Electrical conductivity of water 10 milliSiemens per centimeter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000692 conductivity -diss_inorg_nitro WaterInterface dissolved inorganic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of dissolved inorganic nitrogen 761 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000698 dissolved inorganic nitrogen -diss_inorg_phosp WaterInterface dissolved inorganic phosphorus measurement value microgram per liter, milligram per liter, parts per million 1 Concentration of dissolved inorganic phosphorus in the sample 56.5 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000106 dissolved inorganic phosphorus -down_par WaterInterface downward PAR measurement value microEinstein per square meter per second, microEinstein per square centimeter per second 1 Visible waveband radiance and irradiance measurements in the water column 28.71 microEinstein per square meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000703 downward PAR -fluor WaterInterface fluorescence measurement value milligram chlorophyll a per cubic meter, volts 1 Raw or converted fluorescence of water 2.5 volts false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000704 fluorescence -light_intensity WaterInterface light intensity measurement value lux 1 Measurement of light intensity 0.3 lux false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000706 light intensity -part_org_nitro WaterInterface particulate organic nitrogen measurement value microgram per liter, micromole per liter 1 Concentration of particulate organic nitrogen 0.3 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000719 particulate organic nitrogen -photon_flux WaterInterface photon flux measurement value number of photons per second per unit area 1 Measurement of photon flux 3.926 micromole photons per second per square meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000725 photon flux -primary_prod WaterInterface primary production measurement value milligram per cubic meter per day, gram per square meter per day 1 Measurement of primary production, generally measured as isotope uptake 100 milligram per cubic meter per day false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000728 primary production -soluble_react_phosp WaterInterface soluble reactive phosphorus measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of soluble reactive phosphorus 0.1 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000738 soluble reactive phosphorus -suspend_part_matter WaterInterface suspended particulate matter measurement value milligram per liter 1 Concentration of suspended particulate matter 0.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000741 suspended particulate matter tot_diss_nitro WaterInterface total dissolved nitrogen measurement value microgram per liter 1 Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen 40 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000744 total dissolved nitrogen tot_inorg_nitro WaterInterface total inorganic nitrogen measurement value microgram per liter 1 Total inorganic nitrogen content 40 microgram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000745 total inorganic nitrogen +tot_nitro WaterInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration tot_part_carb WaterInterface total particulate carbon measurement value microgram per liter, micromole per liter 1 Total particulate carbon content 35 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000747 total particulate carbon +turbidity WaterInterface turbidity measurement value formazin turbidity unit, formazin nephelometric units 1 Measure of the amount of cloudiness or haziness in water caused by individual particles 0.3 nephelometric turbidity units false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000191 turbidity water_current WaterInterface water current measurement value cubic meter per second, knots 1 Measurement of magnitude and direction of flow within a fluid 10 cubic meter per second false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000203 water current -size_frac WaterInterface size fraction selected filter size value range Filtering pore size used in sample preparation 0-0.22 micrometer false string MIXS:0000017 {float}-{float} {unit} size fraction selected -samp_store_dur WaterInterface sample storage duration duration 1 Duration for which the sample was stored P1Y6M false string MIXS:0000116 {duration} sample storage duration -sodium WaterInterface sodium measurement value milligram per liter, parts per million 1 Sodium concentration in the sample 10.5 milligram per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000428 sodium -sulfide WaterInterface sulfide measurement value micromole per liter, milligram per liter, parts per million 1 Concentration of sulfide in the sample 2 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000424 sulfide -tot_nitro WaterInterface total nitrogen concentration measurement value microgram per liter, micromole per liter, milligram per liter 1 Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen 50 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000102 total nitrogen concentration -collection_date WaterInterface collection date date and time The date of sampling 2021-04-15|2021-04|2021 false MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only|Use modified term (amended definition) ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ string true MIXS:0000011 {date, arbitrary precision} collection date -geo_loc_name WaterInterface geographic location (country and/or sea,region) country or sea name (INSDC or GAZ): region(GAZ), specific location name The geographical origin of the sample as defined by the country or sea name followed by specific region name. USA: Maryland, Bethesda false string MIXS:0000010 {term}: {term}, {text} geographic location (country and/or sea,region) -lat_lon WaterInterface This is currently a required field but it's not clear if this should be required for human hosts false required where? ^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string MIXS:0000009 {float} {float} geographic location (latitude and longitude) -elev WaterInterface All elevations must be reported in meters. Provide the numerical portion only. Elevation 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. 100 false float MIXS:0000093 elevation, meters -samp_store_temp WaterInterface sample storage temperature measurement value degree Celsius 1 Temperature at which sample was stored, e.g. -80 degree Celsius -80 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000110 sample storage temperature -depth WaterInterface depth measurement value All depths must be reported in meters. Provide the numerical portion only. The 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. 0 to 0.1|1 false Use modified term ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ string true MIXS:0000018 {float}|{float}-{float} depth, meters -size_frac_low WaterInterface size-fraction lower threshold value micrometer 1 Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample 0.2 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000735 size-fraction lower threshold -size_frac_up WaterInterface size-fraction upper threshold value micrometer 1 Refers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample 20 micrometer false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000736 size-fraction upper threshold -samp_mat_process WaterInterface sample material processing text A 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. filtering of seawater|storing samples in ethanol false string MIXS:0000016 {text} sample material processing -samp_collec_device WaterInterface sample collection device device name The 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). swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713] false string MIXS:0000002 {termLabel} {[termID]}|{text} sample collection device -samp_collec_method WaterInterface sample collection method PMID,DOI,url , or text The method employed for collecting the sample. swabbing false string MIXS:0001225 {PMID}|{DOI}|{URL}|{text} sample collection method -chem_administration WaterInterface chemical administration CHEBI;timestamp m List 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 agar [CHEBI:2509];2018-05-11|agar [CHEBI:2509];2018-05-22|agar [CHEBI:2509];2018-05 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\];([\+-]?\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)?)?)?)?$ string true MIXS:0000751 {termLabel} {[termID]};{timestamp} chemical administration -samp_size WaterInterface amount or size of sample collected measurement value millliter, gram, milligram, liter The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. 5 liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000001 amount or size of sample collected -rel_to_oxygen WaterInterface relationship to oxygen enumeration Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments aerobe false rel_to_oxygen_enum MIXS:0000015 relationship to oxygen -alt WaterInterface altitude measurement value Altitude 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 100 meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000094 altitude -ph WaterInterface pH measurement value 1 Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid 7.2 false double MIXS:0001001 pH -experimental_factor WaterInterface experimental factor text or EFO and/or OBI Experimental 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 time series design [EFO:0001779] false string MIXS:0000008 {termLabel} {[termID]}|{text} experimental factor -horizon_meth WaterInterface soil horizon method PMID,DOI or url 1 Reference or method used in determining the horizon false string MIXS:0000321 {PMID}|{DOI}|{URL} soil horizon method -misc_param WaterInterface miscellaneous parameter parameter name;measurement value m Any other measurement performed or parameter collected, that is not listed here Bicarbonate ion concentration;2075 micromole per kilogram false ^([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+\|)*([^;\t\r\x0A]+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? [^;\t\r\x0A]+)$ string MIXS:0000752 {text};{float} {unit} miscellaneous parameter -oxy_stat_samp WaterInterface Oxygenation status of sample false this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration|this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration rel_to_oxygen_enum MIXS:0000753 oxygenation status of sample -temp WaterInterface temperature measurement value degree Celsius Temperature of the sample at the time of sampling. 25 degree Celsius false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000113 temperature -ph_meth WaterInterface This can include a link to the instrument used or a citation for the method. Reference or method used in determining ph https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 false string MIXS:0001106 {PMID}|{DOI}|{URL} pH method -carb_nitro_ratio WaterInterface carbon/nitrogen ratio measurement value 1 Ratio of amount or concentrations of carbon to nitrogen 0.417361111 false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ float MIXS:0000310 carbon/nitrogen ratio -org_matter WaterInterface organic matter measurement value microgram per liter 1 Concentration of organic matter 1.75 milligram per cubic meter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000204 organic matter -org_nitro WaterInterface organic nitrogen measurement value microgram per liter 1 Concentration of organic nitrogen 4 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000205 organic nitrogen -phosphate WaterInterface phosphate measurement value micromole per liter 1 Concentration of phosphate 0.7 micromole per liter false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000505 phosphate -salinity WaterInterface salinity measurement value practical salinity unit, percentage 1 The 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. 25 practical salinity unit false ^[-+]?[0-9]*\.?[0-9]+ +\S.*$ string MIXS:0000183 salinity -analysis_type WaterInterface Select all the data types associated or available for this biosample metagenomics; metabolomics; proteomics true analysis_type_enum true analysis/data type -env_package WaterInterface environmental package MIxS 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 mixs extension false string -sample_link WaterInterface This field allows multiple entries separated by ; (Examples: Soil collected from the field will link with the soil used in an incubation. The soil a plant was grown in links to the plant sample. An original culture sample was transferred to a new vial and generated a new sample) A 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. IGSN:DSJ0284 false "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" [^\:\n\r]+\:[^\:\n\r]+ string true {text}:{text} sample linkage -env_broad_scale WaterInterface Report 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’s 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 false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000012 {termLabel} {[termID]} broad-scale environmental context -env_local_scale WaterInterface Report the entity or entities which are in the sample or specimen’s 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. false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000013 {termLabel} {[termID]} local environmental context -env_medium WaterInterface Report 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). false ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$ string true MIXS:0000014 {termLabel} {[termID]} environmental medium -ecosystem WaterInterface The abiotic factors play a profound role on the type and composition of organisms in a given environment. The GOLD Ecosystem at the top of the five-level classification system is aimed at capturing the broader environment from which an organism or environmental sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated, and Engineered. They represent samples collected from a natural environment or from another organism or from engineered environments like bioreactors respectively. An 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. false string true -ecosystem_category WaterInterface The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial. Ecosystem categories for Host-associated samples can be individual hosts or phyla and for engineered samples it may be manipulated environments like bioreactors, solid waste etc. Ecosystem 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. false string true -ecosystem_type WaterInterface The Aquatic ecosystem category (for example) may have ecosystem types like Marine or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air as different Ecosystem Types. In the case of Host-associated samples, ecosystem type can represent Respiratory system, Digestive system, Roots etc. Ecosystem 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. false string true -ecosystem_subtype WaterInterface Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem subtype category. Ecosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path. false string true -specific_ecosystem WaterInterface Specific ecosystems help to define samples based on very specific characteristics of an environment under the five-level classification system. Specific 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. false string true water_content WaterInterface 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space false string value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? NamedThing a databased entity or concept/class diff --git a/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv b/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv index b27e22aa..6e744203 100644 --- a/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv +++ b/schema_sheets/tsv_in/sheets-for-nmdc-submission-schema_classes.tsv @@ -8,8 +8,8 @@ EmslInterface Emsl emsl dh_interface DhInterface DhMultiviewCommonColumnsMixin HcrCoresInterface Hcr Cores hcr_cores dh_interface DhInterface DhMultiviewCommonColumnsMixin HcrFluidsSwabsInterface Hcr Fluids Swabs hcr_fluids_swabs dh_interface DhInterface DhMultiviewCommonColumnsMixin HostAssociatedInterface Host Associated host_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin -JgiMgInterface JGI MG jgi_mg dh_interface DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_collect_site|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_organisms|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna -JgiMtInterface JGI MT jgi_mt dh_interface DhInterface DhMultiviewCommonColumnsMixin dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_collect_site|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_organisms|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume +JgiMgInterface JGI MG jgi_mg dh_interface DhInterface DhMultiviewCommonColumnsMixin dna_absorb1|dna_absorb2|dna_concentration|dna_cont_type|dna_cont_well|dna_container_id|dna_dnase|dna_isolate_meth|dna_project_contact|dna_samp_id|dna_sample_format|dna_sample_name|dna_seq_project|dna_seq_project_name|dna_seq_project_pi|dna_volume|proposal_dna +JgiMtInterface JGI MT jgi_mt dh_interface DhInterface DhMultiviewCommonColumnsMixin dnase_rna|proposal_rna|rna_absorb1|rna_absorb2|rna_concentration|rna_cont_type|rna_cont_well|rna_container_id|rna_isolate_meth|rna_project_contact|rna_samp_id|rna_sample_format|rna_sample_name|rna_seq_project|rna_seq_project_name|rna_seq_project_pi|rna_volume MiscEnvsInterface Misc Envs misc_envs dh_interface DhInterface DhMultiviewCommonColumnsMixin PlantAssociatedInterface Plant Associated plant_associated dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin SedimentInterface Sediment sediment dh_interface DhInterface DhMultiviewCommonColumnsMixin|SampIdNewTermsMixin diff --git a/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv b/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv index bbdf541a..4952f95e 100644 --- a/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv +++ b/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_import_slots_regardless.tsv @@ -1,126 +1,66 @@ source class source file or URL slot section column order destination class -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml project_id emsl_section 1 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_type emsl_section 2 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_shipped emsl_section 3 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml emsl_store_temp emsl_section 4 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml technical_reps emsl_section 5 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml replicate_number emsl_section 6 EmslInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project jgi_metagenomics_section 1 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project_name jgi_metagenomics_section 2 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_samp_id jgi_metagenomics_section 3 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_sample_name jgi_metagenomics_section 4 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_concentration jgi_metagenomics_section 5 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_volume jgi_metagenomics_section 6 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_absorb1 jgi_metagenomics_section 7 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_absorb2 jgi_metagenomics_section 8 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_container_id jgi_metagenomics_section 9 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_cont_type jgi_metagenomics_section 10 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_cont_well jgi_metagenomics_section 11 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_sample_format jgi_metagenomics_section 12 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_dnase jgi_metagenomics_section 13 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_organisms jgi_metagenomics_section 14 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_collect_site jgi_metagenomics_section 15 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_isolate_meth jgi_metagenomics_section 16 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project_pi jgi_metagenomics_section 17 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_project_contact jgi_metagenomics_section 18 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml proposal_dna jgi_metagenomics_section 19 JgiMgInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project jgi_metatranscriptomics_section 1 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project_name jgi_metatranscriptomics_section 2 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_samp_id jgi_metatranscriptomics_section 3 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_sample_name jgi_metatranscriptomics_section 4 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_concentration jgi_metatranscriptomics_section 5 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_volume jgi_metatranscriptomics_section 6 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_absorb1 jgi_metatranscriptomics_section 7 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_absorb2 jgi_metatranscriptomics_section 8 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_container_id jgi_metatranscriptomics_section 9 JgiMtInterface -Biosample 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https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_collect_site jgi_metatranscriptomics_section 15 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_isolate_meth jgi_metatranscriptomics_section 16 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project_pi jgi_metatranscriptomics_section 17 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_project_contact jgi_metatranscriptomics_section 18 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml proposal_rna jgi_metatranscriptomics_section 19 JgiMtInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkalinity mixs_core_section 1 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkyl_diethers mixs_core_section 2 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml aminopept_act mixs_core_section 3 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ammonium mixs_core_section 4 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bacteria_carb_prod mixs_core_section 5 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biomass mixs_core_section 6 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bishomohopanol mixs_core_section 7 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bromide mixs_core_section 8 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml calcium mixs_core_section 9 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chloride mixs_core_section 10 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chlorophyll mixs_core_section 11 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml density mixs_core_section 12 HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diether_lipids mixs_core_section 13 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_carb_dioxide mixs_core_section 14 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_hydrogen mixs_core_section 15 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_carb mixs_core_section 16 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_org_carb mixs_core_section 17 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_org_nitro mixs_core_section 18 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_oxygen mixs_core_section 19 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml glucosidase_act mixs_core_section 20 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml magnesium mixs_core_section 21 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|SedimentInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mean_frict_vel mixs_core_section 22 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mean_peak_frict_vel mixs_core_section 23 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml methane mixs_core_section 24 AirInterface|BiofilmInterface|SedimentInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml n_alkanes mixs_core_section 25 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrate mixs_core_section 26 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrite mixs_core_section 27 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitro mixs_core_section 28 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_carb mixs_core_section 29 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml organism_count mixs_core_section 30 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml part_org_carb mixs_core_section 31 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml particle_class mixs_core_section 32 SedimentInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml perturbation mixs_core_section 33 AirInterface|BiofilmInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml petroleum_hydrocarb mixs_core_section 34 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phaeopigments mixs_core_section 35 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phosplipid_fatt_acid mixs_core_section 36 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml porosity mixs_core_section 37 HcrCoresInterface|SedimentInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml potassium mixs_core_section 38 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pressure mixs_core_section 39 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml redox_potential mixs_core_section 40 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_loc mixs_core_section 41 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sediment_type mixs_core_section 42 SedimentInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml silicate mixs_core_section 43 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfate mixs_core_section 44 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tidal_stage mixs_core_section 45 SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_depth_water_col mixs_core_section 46 SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml turbidity mixs_core_section 47 BiofilmInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml air_PM_concen mixs_core_section 48 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml barometric_press mixs_core_section 49 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_dioxide mixs_core_section 50 AirInterface|BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_monoxide mixs_core_section 51 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml humidity mixs_core_section 52 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml oxygen mixs_core_section 53 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pollutants mixs_core_section 54 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml solar_irradiance mixs_core_section 55 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ventilation_rate mixs_core_section 56 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ventilation_type mixs_core_section 57 AirInterface|BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml volatile_org_comp mixs_core_section 58 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wind_direction mixs_core_section 59 AirInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wind_speed mixs_core_section 60 AirInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml abs_air_humidity mixs_core_section 61 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml add_recov_method mixs_core_section 289 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml additional_info mixs_core_section 290 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml address mixs_core_section 62 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml adj_room mixs_core_section 63 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml aero_struc mixs_core_section 64 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml agrochem_addition mixs_section 2 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml air_PM_concen mixs_core_section 48 AirInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml air_temp mixs_core_section 65 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml air_temp_regm mixs_modified_section 16 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml al_sat mixs_section 3 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml al_sat_meth mixs_section 4 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkalinity mixs_core_section 1 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkalinity_method mixs_core_section 218 HcrCoresInterface|HcrFluidsSwabsInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkyl_diethers mixs_core_section 2 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alt mixs_modified_section 26 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml aminopept_act mixs_core_section 3 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ammonium mixs_core_section 4 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ammonium_nitrogen mixs_inspired_section 1005 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml amount_light mixs_core_section 66 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml analysis_type sample_id_section 3 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ances_data mixs_core_section 237 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml annual_precpt mixs_section 5 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml annual_temp mixs_section 6 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml antibiotic_regm mixs_core_section 238 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml api mixs_core_section 291 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml arch_struc mixs_core_section 67 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml aromatics_pc mixs_core_section 292 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml asphaltenes_pc mixs_core_section 293 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml atmospheric_data mixs_core_section 219 WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml avg_dew_point mixs_core_section 68 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml avg_occup mixs_core_section 69 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml avg_temp mixs_core_section 70 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bac_prod mixs_core_section 220 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bac_resp mixs_core_section 221 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bacteria_carb_prod mixs_core_section 5 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml barometric_press mixs_core_section 49 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml basin mixs_core_section 294 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bathroom_count mixs_core_section 71 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bedroom_count mixs_core_section 72 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml benzene mixs_core_section 295 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biochem_oxygen_dem mixs_core_section 296 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biocide mixs_core_section 297 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biocide_admin_method mixs_core_section 298 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biol_stat mixs_core_section 239 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biomass mixs_core_section 6 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biotic_regm mixs_modified_section 13 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biotic_relationship mixs_modified_section 22 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bishomohopanol mixs_core_section 7 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml blood_press_diast mixs_core_section 299 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml blood_press_syst mixs_core_section 300 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bromide mixs_core_section 8 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml build_docs mixs_core_section 73 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml build_occup_type mixs_core_section 74 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml building_setting mixs_core_section 75 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml built_struc_age mixs_core_section 76 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml built_struc_set mixs_core_section 77 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml built_struc_type mixs_core_section 78 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml calcium mixs_core_section 9 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_dioxide mixs_core_section 50 AirInterface|BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_monoxide mixs_core_section 51 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_nitro_ratio mixs_section 44 BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_area mixs_core_section 79 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_cond mixs_core_section 80 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_finish_mat mixs_core_section 81 BuiltEnvInterface @@ -129,9 +69,58 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_thermal_mass mixs_core_section 84 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_type mixs_core_section 85 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ceil_water_mold mixs_core_section 86 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_administration mixs_modified_section 17 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_mutagen mixs_core_section 240 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_oxygen_dem mixs_core_section 301 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_treat_method mixs_core_section 302 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_treatment mixs_core_section 303 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chloride mixs_core_section 10 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chlorophyll mixs_core_section 11 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml climate_environment mixs_modified_section 19 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_date mixs_modified_section 3 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_date_inc mixs_inspired_section 2 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_time mixs_inspired_section 1 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_time_inc mixs_inspired_section 3 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml conduc mixs_core_section 222 WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cool_syst_id mixs_core_section 87 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml crop_rotation mixs_section 7 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cult_root_med mixs_core_section 241 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_land_use mixs_section 8 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_vegetation mixs_section 9 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_vegetation_meth mixs_section 10 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml date_last_rain mixs_core_section 88 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml density mixs_core_section 12 HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml depos_env mixs_core_section 304 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml depth mixs_modified_section 9 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dew_point mixs_core_section 89 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diether_lipids mixs_core_section 13 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_carb_dioxide mixs_core_section 14 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_hydrogen mixs_core_section 15 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_carb mixs_core_section 16 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_nitro mixs_core_section 223 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_phosp mixs_core_section 224 HcrCoresInterface|HcrFluidsSwabsInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_iron mixs_core_section 305 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_org_carb mixs_core_section 17 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_org_nitro mixs_core_section 18 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_oxygen mixs_core_section 19 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_oxygen_fluid mixs_core_section 306 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_absorb1 jgi_metagenomics_section 7 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_absorb2 jgi_metagenomics_section 8 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_concentration jgi_metagenomics_section 5 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_cont_type jgi_metagenomics_section 10 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_cont_well jgi_metagenomics_section 11 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_container_id jgi_metagenomics_section 9 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_dnase jgi_metagenomics_section 13 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_isolate_meth jgi_metagenomics_section 16 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_project_contact jgi_metagenomics_section 18 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_samp_id jgi_metagenomics_section 3 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_sample_format jgi_metagenomics_section 12 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_sample_name jgi_metagenomics_section 4 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project jgi_metagenomics_section 1 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project_name jgi_metagenomics_section 2 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_seq_project_pi jgi_metagenomics_section 17 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dna_volume jgi_metagenomics_section 6 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml dnase_rna jgi_metatranscriptomics_section 13 JgiMtInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_comp_type mixs_core_section 90 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_cond mixs_core_section 91 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_direct mixs_core_section 92 BuiltEnvInterface @@ -143,16 +132,40 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_type_metal mixs_core_section 98 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_type_wood mixs_core_section 99 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml door_water_mold mixs_core_section 100 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml down_par mixs_core_section 225 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml drainage_class mixs_section 11 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml drawings mixs_core_section 101 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem sample_id_section 9 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_category sample_id_section 10 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_subtype sample_id_section 12 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_type sample_id_section 11 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml efficiency_percent mixs_core_section 307 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml elev mixs_modified_section 6 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml elevator mixs_core_section 102 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml emsl_store_temp emsl_section 4 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml emulsions mixs_core_section 308 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_broad_scale sample_id_section 6 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_local_scale sample_id_section 7 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_medium sample_id_section 8 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_package sample_id_section 4 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml escalator mixs_core_section 103 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ethylbenzene mixs_core_section 309 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml exp_duct mixs_core_section 104 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml exp_pipe mixs_core_section 105 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml experimental_factor mixs_section 12 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml experimental_factor_other mixs_inspired_section 7 SoilMixsInspiredMixin|SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ext_door mixs_core_section 106 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ext_wall_orient mixs_core_section 107 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ext_window_orient mixs_core_section 108 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml extreme_event mixs_section 13 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fao_class mixs_section 14 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fertilizer_regm mixs_core_section 242 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml field mixs_core_section 310 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml filter_method mixs_inspired_section 6 SoilMixsInspiredMixin|SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml filter_type mixs_core_section 109 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fire mixs_section 15 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fireplace_type mixs_core_section 110 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml flooding mixs_section 16 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_age mixs_core_section 111 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_area mixs_core_section 112 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_cond mixs_core_section 113 BuiltEnvInterface @@ -161,36 +174,196 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_struc mixs_core_section 116 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_thermal_mass mixs_core_section 117 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml floor_water_mold mixs_core_section 118 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fluor mixs_core_section 226 WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml freq_clean mixs_core_section 119 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml freq_cook mixs_core_section 120 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fungicide_regm mixs_core_section 243 PlantAssociatedInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml furniture mixs_core_section 121 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gaseous_environment mixs_modified_section 20 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gaseous_substances mixs_core_section 311 WastewaterSludgeInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gender_restroom mixs_core_section 122 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml genetic_mod mixs_core_section 244 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml geo_loc_name mixs_modified_section 4 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml glucosidase_act mixs_core_section 20 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gravidity mixs_core_section 312 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gravity mixs_core_section 245 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_facil mixs_modified_section 1 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_habit mixs_core_section 246 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_hormone_regm mixs_core_section 247 PlantAssociatedInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hall_count mixs_core_section 123 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml handidness mixs_core_section 124 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hc_produced mixs_core_section 313 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr mixs_core_section 314 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_fw_salinity mixs_core_section 315 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_geol_age mixs_core_section 316 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_pressure mixs_core_section 317 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_temp mixs_core_section 318 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heat_cool_type mixs_core_section 125 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heat_deliv_loc mixs_core_section 126 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heat_sys_deliv_meth mixs_core_section 127 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heat_system_id mixs_core_section 128 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heavy_metals mixs_section 17 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heavy_metals_meth mixs_section 18 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml height_carper_fiber mixs_core_section 129 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indoor_space mixs_core_section 130 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indoor_surf mixs_core_section 131 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml inside_lux mixs_core_section 132 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml int_wall_cond mixs_core_section 133 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml last_clean mixs_core_section 134 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_type mixs_core_section 135 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml max_occup mixs_core_section 136 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mech_struc mixs_core_section 137 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_pets mixs_core_section 138 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_plants mixs_core_section 139 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_resident mixs_core_section 140 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_density_samp mixs_core_section 141 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_document mixs_core_section 142 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_samp mixs_core_section 143 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pres_animal_insect mixs_core_section 144 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml quad_pos mixs_core_section 145 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_air_humidity mixs_core_section 146 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_humidity_out mixs_core_section 147 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_samp_loc mixs_core_section 148 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml herbicide_regm mixs_core_section 248 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml horizon_meth mixs_section 19 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_age mixs_core_section 249 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_habitat mixs_core_section 319 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_product mixs_core_section 320 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_site mixs_core_section 321 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_temp mixs_core_section 322 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_color mixs_core_section 323 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_common_name mixs_core_section 250 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_diet mixs_core_section 324 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_dry_mass mixs_core_section 251 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_family_relation mixs_core_section 325 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_genotype mixs_core_section 252 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_growth_cond mixs_core_section 326 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_height mixs_core_section 253 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_last_meal mixs_core_section 327 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_length mixs_core_section 254 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_life_stage mixs_core_section 255 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_phenotype mixs_core_section 256 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_sex mixs_core_section 328 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_shape mixs_core_section 329 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_subject_id mixs_core_section 330 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_subspecf_genlin mixs_core_section 257 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_substrate mixs_core_section 331 HostAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_symbiont mixs_core_section 258 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_taxid mixs_core_section 259 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_tot_mass mixs_core_section 260 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_wet_mass mixs_core_section 261 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml humidity mixs_core_section 52 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml humidity_regm mixs_modified_section 21 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indoor_space mixs_core_section 130 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indoor_surf mixs_core_section 131 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indust_eff_percent mixs_core_section 332 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml inorg_particles mixs_core_section 333 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml inside_lux mixs_core_section 132 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml int_wall_cond mixs_core_section 133 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml isotope_exposure mixs_inspired_section 16 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml iw_bt_date_well mixs_core_section 334 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml iwf mixs_core_section 335 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml last_clean mixs_core_section 134 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lat_lon mixs_modified_section 5 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lbc_thirty mixs_inspired_section 1001 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lbceq mixs_inspired_section 1002 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_intensity mixs_core_section 227 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_regm mixs_modified_section 24 PlantAssociatedInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_type mixs_core_section 135 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml link_class_info mixs_section 20 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml link_climate_info mixs_section 21 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lithology mixs_core_section 336 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml local_class mixs_section 22 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml local_class_meth mixs_section 24 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml magnesium mixs_core_section 21 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|SedimentInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml manganese mixs_inspired_section 1003 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml max_occup mixs_core_section 136 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mean_frict_vel mixs_core_section 22 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mean_peak_frict_vel mixs_core_section 23 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mech_struc mixs_core_section 137 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mechanical_damage mixs_core_section 262 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml methane mixs_core_section 24 AirInterface|BiofilmInterface|SedimentInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_c_meth mixs_inspired_section 11 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_c_meth mixs_inspired_section 1004 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_meth mixs_section 43 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_n_meth mixs_inspired_section 13 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_n_meth mixs_inspired_section 1004 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass mixs_section 42 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_c mixs_inspired_section 10 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_c mixs_inspired_section 1004 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_n mixs_inspired_section 12 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_n mixs_inspired_section 1004 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mineral_nutr_regm mixs_core_section 263 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml misc_param mixs_section 23 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml n_alkanes mixs_core_section 25 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrate mixs_core_section 26 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrate_nitrogen mixs_inspired_section 1006 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrite mixs_core_section 27 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrite_nitrogen mixs_inspired_section 1007 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitro mixs_core_section 28 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_microb_biomass mixs_inspired_section 8 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_microb_biomass_method mixs_inspired_section 9 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_min_nutr_regm mixs_core_section 264 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_pets mixs_core_section 138 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_plants mixs_core_section 139 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml number_resident mixs_core_section 140 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_density_samp mixs_core_section 141 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_document mixs_core_section 142 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml occup_samp mixs_core_section 143 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_carb mixs_core_section 29 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_count_qpcr_info mixs_core_section 337 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_matter mixs_section 45 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_nitro mixs_section 46 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_nitro_method mixs_inspired_section 14 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_particles mixs_core_section 338 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml organism_count mixs_core_section 30 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml other_treatment mixs_inspired_section 15 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml owc_tvdss mixs_core_section 339 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml oxy_stat_samp mixs_section 25 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml oxygen mixs_core_section 53 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml part_org_carb mixs_core_section 31 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml part_org_nitro mixs_core_section 228 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml particle_class mixs_core_section 32 SedimentInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml permeability mixs_core_section 340 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml perturbation mixs_core_section 33 AirInterface|BiofilmInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pesticide_regm mixs_core_section 265 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml petroleum_hydrocarb mixs_core_section 34 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph mixs_modified_section 27 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph_meth mixs_section 41 SoilInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph_regm mixs_core_section 266 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phaeopigments mixs_core_section 35 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phosphate mixs_section 53 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phosplipid_fatt_acid mixs_core_section 36 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml photon_flux mixs_core_section 229 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_growth_med mixs_core_section 267 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_product mixs_core_section 268 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_sex mixs_core_section 269 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_struc mixs_core_section 270 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pollutants mixs_core_section 54 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml porosity mixs_core_section 37 HcrCoresInterface|SedimentInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml potassium mixs_core_section 38 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pour_point mixs_core_section 341 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pre_treatment mixs_core_section 342 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pres_animal_insect mixs_core_section 144 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pressure mixs_core_section 39 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prev_land_use_meth mixs_section 26 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml previous_land_use mixs_section 27 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml primary_prod mixs_core_section 230 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml primary_treatment mixs_core_section 343 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prod_rate mixs_core_section 344 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prod_start_date mixs_core_section 345 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml profile_position mixs_section 28 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml project_id emsl_section 1 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml proposal_dna jgi_metagenomics_section 19 JgiMgInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml proposal_rna jgi_metatranscriptomics_section 19 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml quad_pos mixs_core_section 145 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml radiation_regm mixs_core_section 271 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rainfall_regm mixs_core_section 272 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml reactor_type mixs_core_section 346 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml redox_potential mixs_core_section 40 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_air_humidity mixs_core_section 146 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_humidity_out mixs_core_section 147 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_samp_loc mixs_core_section 148 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_to_oxygen mixs_modified_section 23 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml replicate_number emsl_section 6 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml reservoir mixs_core_section 347 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml resins_pc mixs_core_section 348 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_absorb1 jgi_metatranscriptomics_section 7 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_absorb2 jgi_metatranscriptomics_section 8 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_concentration jgi_metatranscriptomics_section 5 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_cont_type jgi_metatranscriptomics_section 10 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_cont_well jgi_metatranscriptomics_section 11 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_container_id jgi_metatranscriptomics_section 9 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_isolate_meth jgi_metatranscriptomics_section 16 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_project_contact jgi_metatranscriptomics_section 18 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_samp_id jgi_metatranscriptomics_section 3 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_sample_format jgi_metatranscriptomics_section 12 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_sample_name jgi_metatranscriptomics_section 4 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project jgi_metatranscriptomics_section 1 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project_name jgi_metatranscriptomics_section 2 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_seq_project_pi jgi_metatranscriptomics_section 17 JgiMtInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rna_volume jgi_metatranscriptomics_section 6 JgiMtInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_air_exch_rate mixs_core_section 149 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_architec_elem mixs_core_section 150 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_condt mixs_core_section 151 BuiltEnvInterface @@ -209,34 +382,138 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_vol mixs_core_section 164 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_wall_share mixs_core_section 165 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml room_window_count mixs_core_section 166 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_cond mixs_core_section 273 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_carbon mixs_core_section 274 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_macronutr mixs_core_section 275 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_micronutr mixs_core_section 276 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_ph mixs_core_section 277 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_regl mixs_core_section 278 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_solid mixs_core_section 279 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_suppl mixs_core_section 280 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salinity mixs_section 54 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salinity_meth mixs_section 55 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salt_regm mixs_core_section 281 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_capt_status mixs_core_section 282 HostAssociatedInterface|PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collec_device mixs_modified_section 14 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collec_method mixs_modified_section 15 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collect_point mixs_core_section 349 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_dis_stage mixs_core_section 283 HostAssociatedInterface|PlantAssociatedInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_floor mixs_core_section 167 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_loc_corr_rate mixs_core_section 350 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_mat_process mixs_modified_section 12 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_md mixs_core_section 351 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_name sample_id_section 1 DhMultiviewCommonColumnsMixin +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_preserv mixs_core_section 352 HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_room_id mixs_core_section 168 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_size mixs_modified_section 18 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_sort_meth mixs_core_section 169 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_dur mixs_core_section 353 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_loc mixs_core_section 41 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_temp mixs_modified_section 7 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_subtype mixs_core_section 354 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_time_out mixs_core_section 170 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_transport_cond mixs_core_section 355 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_tvdss mixs_core_section 356 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_type mixs_core_section 357 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_weather mixs_core_section 171 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_well_name mixs_core_section 358 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_link sample_id_section 5 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_shipped emsl_section 3 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_type emsl_section 2 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml saturates_pc mixs_core_section 359 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season mixs_core_section 172 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_environment mixs_core_section 284 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_precpt mixs_section 29 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_temp mixs_section 30 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_use mixs_core_section 173 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml secondary_treatment mixs_core_section 360 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sediment_type mixs_core_section 42 SedimentInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sewage_type mixs_core_section 361 WastewaterSludgeInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml shad_dev_water_mold mixs_core_section 174 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml shading_device_cond mixs_core_section 175 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml shading_device_loc mixs_core_section 176 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml shading_device_mat mixs_core_section 177 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml shading_device_type mixs_core_section 178 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sieving mixs_modified_section 8 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml silicate mixs_core_section 43 BiofilmInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac mixs_core_section 285 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac_low mixs_modified_section 10 SoilInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac_up mixs_modified_section 11 SoilInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml slope_aspect mixs_section 1 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml slope_gradient mixs_section 31 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sludge_retent_time mixs_core_section 362 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sodium mixs_core_section 363 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_horizon mixs_section 32 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_text_measure mixs_section 33 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_texture_meth mixs_section 34 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_type mixs_section 35 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_type_meth mixs_section 36 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml solar_irradiance mixs_core_section 55 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_inorg_mat mixs_core_section 364 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_org_mat mixs_core_section 365 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_react_phosp mixs_core_section 231 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml source_mat_id sample_id_section 2 DhMultiviewCommonColumnsMixin Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml space_typ_state mixs_core_section 179 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml specific mixs_core_section 180 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml specific_ecosystem sample_id_section 13 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml specific_humidity mixs_core_section 181 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_dep_env mixs_core_section 366 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_geol_age mixs_core_section 367 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_kerog_type mixs_core_section 368 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_lithology mixs_core_section 369 HcrCoresInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml standing_water_regm mixs_core_section 286 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml start_date_inc mixs_inspired_section 4 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml start_time_inc mixs_inspired_section 5 SoilMixsInspiredMixin|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml store_cond mixs_modified_section 2 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml substructure_type mixs_core_section 182 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfate mixs_core_section 44 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfate_fw mixs_core_section 370 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfide mixs_core_section 371 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_air_cont mixs_core_section 183 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_humidity mixs_core_section 184 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_material mixs_core_section 185 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_moisture mixs_core_section 186 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_moisture_ph mixs_core_section 187 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml surf_temp mixs_core_section 188 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml suspend_part_matter mixs_core_section 232 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml suspend_solids mixs_core_section 372 HcrCoresInterface|HcrFluidsSwabsInterface|WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tan mixs_core_section 373 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml technical_reps emsl_section 5 EmslInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml temp mixs_section 37 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml temp_out mixs_core_section 189 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tertiary_treatment mixs_core_section 374 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tidal_stage mixs_core_section 45 SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tillage mixs_section 38 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tiss_cult_growth_med mixs_core_section 287 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml toluene mixs_core_section 375 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_carb mixs_section 47 BiofilmInterface|SedimentInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_depth_water_col mixs_core_section 46 SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_diss_nitro mixs_core_section 233 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_inorg_nitro mixs_core_section 234 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_iron mixs_core_section 376 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro mixs_core_section 377 HcrCoresInterface|HcrFluidsSwabsInterface|WastewaterSludgeInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro_cont_meth mixs_section 49 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro_content mixs_section 48 BiofilmInterface|SedimentInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_org_c_meth mixs_section 51 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_org_carb mixs_section 50 BiofilmInterface|SedimentInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_part_carb mixs_core_section 235 WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_phosp mixs_section 52 HcrCoresInterface|HcrFluidsSwabsInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_phosphate mixs_core_section 378 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_sulfur mixs_core_section 379 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml train_line mixs_core_section 190 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml train_stat_loc mixs_core_section 191 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml train_stop_loc mixs_core_section 192 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml typ_occup_density mixs_core_section 193 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vis_media mixs_core_section 194 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml turbidity mixs_core_section 47 BiofilmInterface|SedimentInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tvdss_of_hcr_press mixs_core_section 380 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tvdss_of_hcr_temp mixs_core_section 381 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml typ_occup_density mixs_core_section 193 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ventilation_rate mixs_core_section 56 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ventilation_type mixs_core_section 57 AirInterface|BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vfa mixs_core_section 382 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vfa_fw mixs_core_section 383 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vis_media mixs_core_section 194 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml viscosity mixs_core_section 384 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml volatile_org_comp mixs_core_section 58 AirInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_area mixs_core_section 195 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_const_type mixs_core_section 196 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_finish_mat mixs_core_section 197 BuiltEnvInterface @@ -246,9 +523,20 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_texture mixs_core_section 201 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_thermal_mass mixs_core_section 202 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wall_water_mold mixs_core_section 203 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wastewater_type mixs_core_section 385 WastewaterSludgeInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_cont_soil_meth mixs_section 40 SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_content mixs_section 39 BiofilmInterface|SedimentInterface|SoilInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_current mixs_core_section 236 MiscEnvsInterface|WaterInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_cut mixs_core_section 386 HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_feat_size mixs_core_section 204 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_feat_type mixs_core_section 205 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_prod_rate mixs_core_section 387 HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_temp_regm mixs_core_section 288 PlantAssociatedInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml watering_regm mixs_modified_section 25 PlantAssociatedInterface|SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml weekday mixs_core_section 206 BuiltEnvInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml win mixs_core_section 388 HcrCoresInterface|HcrFluidsSwabsInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wind_direction mixs_core_section 59 AirInterface +Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wind_speed mixs_core_section 60 AirInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_cond mixs_core_section 207 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_cover mixs_core_section 208 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_horiz_pos mixs_core_section 209 BuiltEnvInterface @@ -260,297 +548,5 @@ Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/n Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_type mixs_core_section 215 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_vert_pos mixs_core_section 216 BuiltEnvInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml window_water_mold mixs_core_section 217 BuiltEnvInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alkalinity_method mixs_core_section 218 HcrCoresInterface|HcrFluidsSwabsInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml atmospheric_data mixs_core_section 219 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bac_prod mixs_core_section 220 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml bac_resp mixs_core_section 221 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml conduc mixs_core_section 222 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_nitro mixs_core_section 223 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_inorg_phosp mixs_core_section 224 HcrCoresInterface|HcrFluidsSwabsInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml down_par mixs_core_section 225 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fluor mixs_core_section 226 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_intensity mixs_core_section 227 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml part_org_nitro mixs_core_section 228 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml photon_flux mixs_core_section 229 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml primary_prod mixs_core_section 230 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_react_phosp mixs_core_section 231 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml suspend_part_matter mixs_core_section 232 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_diss_nitro mixs_core_section 233 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_inorg_nitro mixs_core_section 234 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_part_carb mixs_core_section 235 WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_current mixs_core_section 236 MiscEnvsInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ances_data mixs_core_section 237 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml antibiotic_regm mixs_core_section 238 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biol_stat mixs_core_section 239 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_mutagen mixs_core_section 240 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cult_root_med mixs_core_section 241 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fertilizer_regm mixs_core_section 242 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fungicide_regm mixs_core_section 243 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml genetic_mod mixs_core_section 244 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gravity mixs_core_section 245 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_habit mixs_core_section 246 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_hormone_regm mixs_core_section 247 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml herbicide_regm mixs_core_section 248 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_age mixs_core_section 249 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_common_name mixs_core_section 250 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_dry_mass mixs_core_section 251 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_genotype mixs_core_section 252 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_height mixs_core_section 253 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_length mixs_core_section 254 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_life_stage mixs_core_section 255 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_phenotype mixs_core_section 256 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_subspecf_genlin mixs_core_section 257 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_symbiont mixs_core_section 258 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_taxid mixs_core_section 259 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_tot_mass mixs_core_section 260 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_wet_mass mixs_core_section 261 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mechanical_damage mixs_core_section 262 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml mineral_nutr_regm mixs_core_section 263 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_min_nutr_regm mixs_core_section 264 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pesticide_regm mixs_core_section 265 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph_regm mixs_core_section 266 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_growth_med mixs_core_section 267 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_product mixs_core_section 268 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_sex mixs_core_section 269 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml plant_struc mixs_core_section 270 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml radiation_regm mixs_core_section 271 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rainfall_regm mixs_core_section 272 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_cond mixs_core_section 273 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_carbon mixs_core_section 274 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_macronutr mixs_core_section 275 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_micronutr mixs_core_section 276 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_ph mixs_core_section 277 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_regl mixs_core_section 278 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_solid mixs_core_section 279 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml root_med_suppl mixs_core_section 280 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salt_regm mixs_core_section 281 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_capt_status mixs_core_section 282 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_dis_stage mixs_core_section 283 HostAssociatedInterface|PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_environment mixs_core_section 284 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac mixs_core_section 285 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml standing_water_regm mixs_core_section 286 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tiss_cult_growth_med mixs_core_section 287 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_temp_regm mixs_core_section 288 PlantAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml add_recov_method mixs_core_section 289 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml additional_info mixs_core_section 290 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml api mixs_core_section 291 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml aromatics_pc mixs_core_section 292 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml asphaltenes_pc mixs_core_section 293 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml basin mixs_core_section 294 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml benzene mixs_core_section 295 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biochem_oxygen_dem mixs_core_section 296 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biocide mixs_core_section 297 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biocide_admin_method mixs_core_section 298 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml blood_press_diast mixs_core_section 299 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml blood_press_syst mixs_core_section 300 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_oxygen_dem mixs_core_section 301 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_treat_method mixs_core_section 302 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_treatment mixs_core_section 303 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml depos_env mixs_core_section 304 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_iron mixs_core_section 305 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml diss_oxygen_fluid mixs_core_section 306 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml efficiency_percent mixs_core_section 307 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml emulsions mixs_core_section 308 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ethylbenzene mixs_core_section 309 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml field mixs_core_section 310 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gaseous_substances mixs_core_section 311 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gravidity mixs_core_section 312 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hc_produced mixs_core_section 313 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr mixs_core_section 314 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_fw_salinity mixs_core_section 315 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_geol_age mixs_core_section 316 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_pressure mixs_core_section 317 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml hcr_temp mixs_core_section 318 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_habitat mixs_core_section 319 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_product mixs_core_section 320 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_site mixs_core_section 321 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_body_temp mixs_core_section 322 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_color mixs_core_section 323 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_diet mixs_core_section 324 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_family_relation mixs_core_section 325 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_growth_cond mixs_core_section 326 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_last_meal mixs_core_section 327 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_sex mixs_core_section 328 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_shape mixs_core_section 329 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_subject_id mixs_core_section 330 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml host_substrate mixs_core_section 331 HostAssociatedInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml indust_eff_percent mixs_core_section 332 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml inorg_particles mixs_core_section 333 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml iw_bt_date_well mixs_core_section 334 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml iwf mixs_core_section 335 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lithology mixs_core_section 336 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_count_qpcr_info mixs_core_section 337 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_particles mixs_core_section 338 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml owc_tvdss mixs_core_section 339 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml permeability mixs_core_section 340 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pour_point mixs_core_section 341 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml pre_treatment mixs_core_section 342 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml primary_treatment mixs_core_section 343 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prod_rate mixs_core_section 344 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prod_start_date mixs_core_section 345 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml reactor_type mixs_core_section 346 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml reservoir mixs_core_section 347 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml resins_pc mixs_core_section 348 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collect_point mixs_core_section 349 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_loc_corr_rate mixs_core_section 350 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_md mixs_core_section 351 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_preserv mixs_core_section 352 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_dur mixs_core_section 353 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_subtype mixs_core_section 354 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_transport_cond mixs_core_section 355 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_tvdss mixs_core_section 356 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_type mixs_core_section 357 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_well_name mixs_core_section 358 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml saturates_pc mixs_core_section 359 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml secondary_treatment mixs_core_section 360 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sewage_type mixs_core_section 361 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sludge_retent_time mixs_core_section 362 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sodium mixs_core_section 363 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_inorg_mat mixs_core_section 364 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soluble_org_mat mixs_core_section 365 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_dep_env mixs_core_section 366 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_geol_age mixs_core_section 367 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_kerog_type mixs_core_section 368 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sr_lithology mixs_core_section 369 HcrCoresInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfate_fw mixs_core_section 370 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sulfide mixs_core_section 371 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml suspend_solids mixs_core_section 372 HcrCoresInterface|HcrFluidsSwabsInterface|WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tan mixs_core_section 373 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tertiary_treatment mixs_core_section 374 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml toluene mixs_core_section 375 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_iron mixs_core_section 376 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro mixs_core_section 377 HcrCoresInterface|HcrFluidsSwabsInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_phosphate mixs_core_section 378 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_sulfur mixs_core_section 379 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tvdss_of_hcr_press mixs_core_section 380 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tvdss_of_hcr_temp mixs_core_section 381 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vfa mixs_core_section 382 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml vfa_fw mixs_core_section 383 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml viscosity mixs_core_section 384 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml wastewater_type mixs_core_section 385 WastewaterSludgeInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_cut mixs_core_section 386 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_prod_rate mixs_core_section 387 HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml win mixs_core_section 388 HcrCoresInterface|HcrFluidsSwabsInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml xylene mixs_core_section 389 HcrCoresInterface|HcrFluidsSwabsInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_time mixs_inspired_section 1 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_date_inc mixs_inspired_section 2 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_time_inc mixs_inspired_section 3 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml start_date_inc mixs_inspired_section 4 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml start_time_inc mixs_inspired_section 5 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml filter_method mixs_inspired_section 6 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml experimental_factor_other mixs_inspired_section 7 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_microb_biomass mixs_inspired_section 8 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml non_microb_biomass_method mixs_inspired_section 9 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_c mixs_inspired_section 10 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_c_meth mixs_inspired_section 11 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_n mixs_inspired_section 12 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_n_meth mixs_inspired_section 13 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_nitro_method mixs_inspired_section 14 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml other_treatment mixs_inspired_section 15 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml isotope_exposure mixs_inspired_section 16 SoilMixsInspiredMixin|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lbc_thirty mixs_inspired_section 1001 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lbceq mixs_inspired_section 1002 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml manganese mixs_inspired_section 1003 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_c_meth mixs_inspired_section 1004 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_n_meth mixs_inspired_section 1004 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_c mixs_inspired_section 1004 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass_n mixs_inspired_section 1004 SoilInterface Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml zinc mixs_inspired_section 1004 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ammonium_nitrogen mixs_inspired_section 1005 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrate_nitrogen mixs_inspired_section 1006 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml nitrite_nitrogen mixs_inspired_section 1007 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml growth_facil mixs_modified_section 1 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml store_cond mixs_modified_section 2 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml collection_date mixs_modified_section 3 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml geo_loc_name mixs_modified_section 4 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml lat_lon mixs_modified_section 5 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml elev mixs_modified_section 6 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_store_temp mixs_modified_section 7 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sieving mixs_modified_section 8 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml depth mixs_modified_section 9 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac_low mixs_modified_section 10 SoilInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml size_frac_up mixs_modified_section 11 SoilInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_mat_process mixs_modified_section 12 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biotic_regm mixs_modified_section 13 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collec_device mixs_modified_section 14 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_collec_method mixs_modified_section 15 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml air_temp_regm mixs_modified_section 16 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml chem_administration mixs_modified_section 17 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_size mixs_modified_section 18 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml climate_environment mixs_modified_section 19 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml gaseous_environment mixs_modified_section 20 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml humidity_regm mixs_modified_section 21 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml biotic_relationship mixs_modified_section 22 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml rel_to_oxygen mixs_modified_section 23 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml light_regm mixs_modified_section 24 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml watering_regm mixs_modified_section 25 PlantAssociatedInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml alt mixs_modified_section 26 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph mixs_modified_section 27 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml slope_aspect mixs_section 1 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml agrochem_addition mixs_section 2 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml al_sat mixs_section 3 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml al_sat_meth mixs_section 4 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml annual_precpt mixs_section 5 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml annual_temp mixs_section 6 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml crop_rotation mixs_section 7 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_land_use mixs_section 8 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_vegetation mixs_section 9 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml cur_vegetation_meth mixs_section 10 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml drainage_class mixs_section 11 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml experimental_factor mixs_section 12 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml extreme_event mixs_section 13 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fao_class mixs_section 14 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml fire mixs_section 15 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml flooding mixs_section 16 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heavy_metals mixs_section 17 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml heavy_metals_meth mixs_section 18 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml horizon_meth mixs_section 19 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml link_class_info mixs_section 20 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml link_climate_info mixs_section 21 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml local_class mixs_section 22 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml misc_param mixs_section 23 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml local_class_meth mixs_section 24 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml oxy_stat_samp mixs_section 25 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml prev_land_use_meth mixs_section 26 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml previous_land_use mixs_section 27 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml profile_position mixs_section 28 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_precpt mixs_section 29 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml season_temp mixs_section 30 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml slope_gradient mixs_section 31 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_horizon mixs_section 32 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_text_measure mixs_section 33 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_texture_meth mixs_section 34 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_type mixs_section 35 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml soil_type_meth mixs_section 36 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml temp mixs_section 37 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tillage mixs_section 38 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_content mixs_section 39 BiofilmInterface|SedimentInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml water_cont_soil_meth mixs_section 40 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ph_meth mixs_section 41 SoilInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml microbial_biomass mixs_section 42 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml micro_biomass_meth mixs_section 43 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml carb_nitro_ratio mixs_section 44 BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_matter mixs_section 45 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml org_nitro mixs_section 46 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_carb mixs_section 47 BiofilmInterface|SedimentInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro_content mixs_section 48 BiofilmInterface|SedimentInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_nitro_cont_meth mixs_section 49 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_org_carb mixs_section 50 BiofilmInterface|SedimentInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_org_c_meth mixs_section 51 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml tot_phosp mixs_section 52 HcrCoresInterface|HcrFluidsSwabsInterface|SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml phosphate mixs_section 53 BiofilmInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salinity mixs_section 54 AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml salinity_meth mixs_section 55 SoilInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml samp_name sample_id_section 1 DhMultiviewCommonColumnsMixin -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml source_mat_id sample_id_section 2 DhMultiviewCommonColumnsMixin -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml analysis_type sample_id_section 3 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_package sample_id_section 4 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml sample_link sample_id_section 5 DhMultiviewCommonColumnsMixin|AirInterface|BiofilmInterface|BuiltEnvInterface|EmslInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|JgiMgInterface|JgiMtInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_broad_scale sample_id_section 6 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_local_scale sample_id_section 7 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml env_medium sample_id_section 8 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem sample_id_section 9 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_category sample_id_section 10 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_type sample_id_section 11 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml ecosystem_subtype sample_id_section 12 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface -Biosample https://raw.githubusercontent.com/microbiomedata/nmdc-schema/b50e66a/nmdc_schema/nmdc_materialized_patterns.yaml specific_ecosystem sample_id_section 13 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface diff --git a/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv b/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv index 59258212..59864103 100644 --- a/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv +++ b/sheets_and_friends/tsv_in/sheets-for-nmdc-submission-schema_modifications_long-dont-mod-water.tsv @@ -1,188 +1,188 @@ class slot action target path LinkML implementation notes value -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth add_attribute comments All depths must be reported in meters. Provide the numerical portion only. -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_device add_attribute comments Report dimensions and details when applicable -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_method add_attribute comments This can be a citation or description -DhMultiviewCommonColumnsMixin samp_name add_attribute comments It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size add_attribute comments This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. -DhMultiviewCommonColumnsMixin source_mat_id add_attribute comments Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date add_attribute notes MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date add_attribute notes Use modified term (amended definition) -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth add_attribute notes Use modified term -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem add_attribute notes range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_category add_attribute notes string or EcosystemCategoryEnum range? -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_subtype add_attribute notes string or EcosystemSubtypeEnum range? -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_type add_attribute notes string or EcosystemTypeEnum range? -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_broad_scale add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_local_scale add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_medium add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" -PlantAssociatedInterface|SoilInterface growth_facil add_attribute notes Removed from description: Alternatively use Crop Ontology (CO) terms -SoilInterface heavy_metals add_attribute notes Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal. -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface lat_lon add_attribute notes This is currently a required field but it's not clear if this should be required for human hosts -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface oxy_stat_samp add_attribute notes this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph add_attribute notes Use modified term -SoilInterface season_precpt add_attribute notes mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average -DhMultiviewCommonColumnsMixin source_mat_id add_attribute notes The source material IS the Globally Unique ID -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface specific_ecosystem add_attribute notes string or SpecificEcosystemEnum range? +PlantAssociatedInterface|SoilInterface air_temp_regm replace_attribute recommended true SoilInterface al_sat add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. -SoilInterface al_sat_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? -SoilInterface annual_precpt add_attribute todos This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot -PlantAssociatedInterface|SoilInterface climate_environment add_attribute todos "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." -SoilInterface cur_vegetation add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Recommend changing this from text value to some kind of ontology? -SoilInterface cur_vegetation_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided. -SoilInterface extreme_event add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot -SoilInterface fire add_attribute todos "is ""to"" acceptable? Is there a better way to request that be written?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" -SoilInterface flooding add_attribute todos "is ""to"" acceptable? Is there a better way to request that be written?|What about if the ""day"" isn't known? Is this ok?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" -PlantAssociatedInterface|SoilInterface gaseous_environment add_attribute todos would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override -SoilInterface heavy_metals add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. -SoilInterface heavy_metals_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot -SoilInterface season_precpt add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|check validation & examples. always mm? so value only? Or value + unit -SoilInterface sieving add_attribute todos check validation and examples -SoilInterface slope_aspect add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot -SoilInterface slope_gradient add_attribute todos Slope is a percent. How does the validation work? Check to correct examples -DhMultiviewCommonColumnsMixin source_mat_id add_attribute todos Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. -BiofilmInterface|SedimentInterface|SoilInterface tot_carb add_attribute todos is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format -BiofilmInterface|SedimentInterface|SoilInterface tot_org_carb add_attribute todos check description. How are they different? -SoilInterface water_cont_soil_meth add_attribute todos Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this? -BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content add_attribute todos value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? SoilInterface al_sat overwrite_examples examples 0.27 +SoilInterface al_sat replace_attribute description The relative abundance of aluminum in the sample +SoilInterface al_sat replace_attribute title aluminum saturation/ extreme unusual properties +SoilInterface al_sat_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? SoilInterface al_sat_meth overwrite_examples examples https://doi.org/10.1371/journal.pone.0176357 +SoilInterface al_sat_meth replace_attribute description Reference or method used in determining Aluminum saturation +SoilInterface al_sat_meth replace_attribute title aluminum saturation method/ extreme unusual properties +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface alt replace_attribute recommended true +SoilInterface annual_precpt add_attribute todos This is no longer matching the listed IRI from GSC, added example. When NMDC has its own slots, map this to the MIxS slot SoilInterface annual_precpt overwrite_examples examples 8.94 inch +PlantAssociatedInterface|SoilInterface biotic_regm replace_attribute recommended true +BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface carb_nitro_ratio replace_attribute range float +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute pattern ^(\S+.*\S+ \[[A-za-z]+:\d+\];[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?\|)*(\S+.*\S+ \[[A-za-z]+:\d+\];[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)$ +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute range string +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute recommended true +PlantAssociatedInterface|SoilInterface climate_environment add_attribute todos "description says ""can include multiple climates"" but multivalued is set to false|add examples, i need to see some examples to add correctly formatted example." +PlantAssociatedInterface|SoilInterface climate_environment replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date add_attribute notes MIxS collection_date accepts (truncated) ISO8601. DH taking arb prec date only +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date add_attribute notes Use modified term (amended definition) AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date overwrite_examples examples 2021-04-15|2021-04|2021 +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute description The date of sampling +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute pattern ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute required true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute string_serialization {date, arbitrary precision} +SoilInterface cur_vegetation add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Recommend changing this from text value to some kind of ontology? SoilInterface cur_vegetation overwrite_examples examples deciduous forest|forest|Bauhinia variegata +SoilInterface cur_vegetation_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|I'm not sure this is a DOI, PMID, or URI. Should pool the community and find out how they accomplish this if provided. SoilInterface cur_vegetation_meth overwrite_examples examples https://doi.org/10.1111/j.1654-109X.2011.01154.x +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth add_attribute comments All depths must be reported in meters. Provide the numerical portion only. +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth add_attribute notes Use modified term AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth overwrite_examples examples 0 to 0.1|1 -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev overwrite_examples examples 225| 0|1250 -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_local_scale overwrite_examples examples canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_medium overwrite_examples examples soil [ENVO:00001998] -SoilInterface|WaterInterface experimental_factor overwrite_examples examples time series design [EFO:0001779] -SoilInterface extreme_event overwrite_examples examples 1980-05-18, volcanic eruption -SoilInterface fire overwrite_examples examples 1871-10-10|1871-10-01 to 1871-10-31 -SoilInterface flooding overwrite_examples examples 1927-04-15|1927-04 to 1927-05 -PlantAssociatedInterface|SoilInterface gaseous_environment overwrite_examples examples CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M -SoilInterface heavy_metals overwrite_examples examples mercury 0.09 micrograms per gram|mercury 0.09 ug/g; chromium 0.03 ug/g -SoilInterface heavy_metals_meth overwrite_examples examples https://doi.org/10.3390/ijms9040434|mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8 -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph_meth overwrite_examples examples https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 -SoilInterface salinity_meth overwrite_examples examples https://doi.org/10.1007/978-1-61779-986-0_28 -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface samp_mat_process overwrite_examples examples filtering of seawater|storing samples in ethanol -DhMultiviewCommonColumnsMixin samp_name overwrite_examples examples Rock core CB1178(5-6) from NSW -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size overwrite_examples examples 5 grams|10 mL -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp overwrite_examples examples -80 Celsius -SoilInterface season_precpt overwrite_examples examples 0.4 inch|10.16 mm -SoilInterface sieving overwrite_examples examples combined 2 cores|4mm sieved|4 mm sieved and homogenized|50 g| 5 cores|2 mm sieved -SoilInterface slope_aspect overwrite_examples examples 35 -SoilInterface slope_gradient overwrite_examples examples 10%|10 %|0.1 -DhMultiviewCommonColumnsMixin source_mat_id overwrite_examples examples IGSN:AU1243|UUID:24f1467a-40f4-11ed-b878-0242ac120002 -BiofilmInterface|SedimentInterface|SoilInterface tot_carb overwrite_examples examples 1 ug/L -SoilInterface tot_nitro_cont_meth overwrite_examples examples https://doi.org/10.2134/agronmonogr9.2.c32|https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo -BiofilmInterface|SedimentInterface|SoilInterface tot_nitro_content overwrite_examples examples 5 mg N/ L -SoilInterface tot_org_c_meth overwrite_examples examples https://doi.org/10.1080/07352680902776556 -BiofilmInterface|SedimentInterface|SoilInterface tot_org_carb overwrite_examples examples 5 mg N/ L -SoilInterface water_cont_soil_meth overwrite_examples examples J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503|https://dec.alaska.gov/applications/spar/webcalc/definitions.htm -BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content overwrite_examples examples 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space -PlantAssociatedInterface|SoilInterface watering_regm overwrite_examples examples 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M|75% water holding capacity; constant -SoilInterface al_sat replace_attribute description The relative abundance of aluminum in the sample -SoilInterface al_sat_meth replace_attribute description Reference or method used in determining Aluminum saturation -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute description The date of sampling -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_broad_scale replace_attribute description In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html -PlantAssociatedInterface|SoilInterface growth_facil replace_attribute description Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface geo_loc_name replace_attribute description The geographical origin of the sample as defined by the country or sea name followed by specific region name. -SoilInterface heavy_metals replace_attribute description Heavy metals present in the sample and their concentrations. -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute description pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid -DhMultiviewCommonColumnsMixin samp_name replace_attribute description A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples. -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp replace_attribute description Temperature at which the sample was stored (degrees are assumed) -SoilInterface slope_aspect replace_attribute description The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. -DhMultiviewCommonColumnsMixin source_mat_id replace_attribute description A globally unique identifier assigned to the biological sample. -SoilInterface store_cond replace_attribute description Explain how the soil sample is stored (fresh/frozen/other). -DhMultiviewCommonColumnsMixin source_mat_id replace_attribute identifier true -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute maximum_value 14 -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute minimum_value expects int?! 0 -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute pattern ^(\S+.*\S+ \[[A-za-z]+:\d+\];[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?\|)*(\S+.*\S+ \[[A-za-z]+:\d+\];[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?)$ -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute pattern ^[12]\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\d|3[01]))?)?$ AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute pattern ^([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? to )?[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$ -SoilInterface fire replace_attribute 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]))?)?)?$ -SoilInterface|WaterInterface organism_count replace_attribute pattern ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other))$ -BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface carb_nitro_ratio replace_attribute range float -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute range string -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute range string AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute required true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute string_serialization {float}|{float}-{float} +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute title depth, meters +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem add_attribute notes range: string or EcosystemEnum? The enum could be dynamic or might be soil biased. SoilInterface ecosystem replace_attribute range EcosystemEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_category add_attribute notes string or EcosystemCategoryEnum range? SoilInterface ecosystem_category replace_attribute range EcosystemCategoryEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_category replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_category replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_subtype add_attribute notes string or EcosystemSubtypeEnum range? SoilInterface ecosystem_subtype replace_attribute range EcosystemSubtypeEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_subtype replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_subtype replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ecosystem_type add_attribute notes string or EcosystemTypeEnum range? SoilInterface ecosystem_type replace_attribute range EcosystemTypeEnum AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface ecosystem_type replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_type replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev overwrite_examples examples 225| 0|1250 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute range float +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute required true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute title elevation, meters +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_broad_scale add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_broad_scale replace_attribute description In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO's biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html SoilInterface env_broad_scale replace_attribute range EnvBroadScaleSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_broad_scale replace_attribute required true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_local_scale add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_local_scale overwrite_examples examples canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336] SoilInterface env_local_scale replace_attribute range EnvLocalScaleSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_local_scale replace_attribute required true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_medium add_attribute notes "range changed to enumeration late in makefile, so this is modified (but ""sample ID"" anyway)" +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface env_medium overwrite_examples examples soil [ENVO:00001998] SoilInterface env_medium replace_attribute range EnvMediumSoilEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_medium replace_attribute required true +SoilInterface|WaterInterface experimental_factor overwrite_examples examples time series design [EFO:0001779] SoilInterface|WaterInterface experimental_factor replace_attribute range string +SoilInterface extreme_event add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot +SoilInterface extreme_event overwrite_examples examples 1980-05-18, volcanic eruption SoilInterface extreme_event replace_attribute range string +SoilInterface extreme_event expected_value date, string +SoilInterface fire add_attribute todos "is ""to"" acceptable? Is there a better way to request that be written?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" +SoilInterface fire overwrite_examples examples 1871-10-10|1871-10-01 to 1871-10-31 +SoilInterface fire replace_attribute 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]))?)?)?$ SoilInterface fire replace_attribute range string +SoilInterface fire expected_value date string +SoilInterface flooding add_attribute todos "is ""to"" acceptable? Is there a better way to request that be written?|What about if the ""day"" isn't known? Is this ok?|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot" +SoilInterface flooding overwrite_examples examples 1927-04-15|1927-04 to 1927-05 SoilInterface flooding replace_attribute range string +SoilInterface flooding expected_value date string +PlantAssociatedInterface|SoilInterface gaseous_environment add_attribute todos would like to see usage examples for this slot. Requiring micromole/L seems too limiting and doesn't match expected_value value|did I do this right? keep the example that's provided and add another? so as to not override +PlantAssociatedInterface|SoilInterface gaseous_environment overwrite_examples examples CO2; 500ppm above ambient; constant|nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M +PlantAssociatedInterface|SoilInterface gaseous_environment replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface geo_loc_name replace_attribute description The geographical origin of the sample as defined by the country or sea name followed by specific region name. +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface geo_loc_name replace_attribute string_serialization {text}: {text}, {text} +PlantAssociatedInterface|SoilInterface growth_facil add_attribute notes Removed from description: Alternatively use Crop Ontology (CO) terms +PlantAssociatedInterface|SoilInterface growth_facil replace_attribute description Type of facility/location where the sample was harvested; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. PlantAssociatedInterface|SoilInterface growth_facil replace_attribute range GrowthFacilEnum +PlantAssociatedInterface|SoilInterface growth_facil replace_attribute required true +SoilInterface heavy_metals add_attribute notes Changed to multi-valued. In MIxS, you add another column to denote multiple heavy metals. We don't have that ability in the submission portal. +SoilInterface heavy_metals add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|Example & validation. Can we make rules that 27% & 27 % & 0.27 will validate?|I think it's weird the way GSC writes the title. I recommend this change. Thoughts? I would argue this isn't an extreme unusual property. It's just a biogeochemical measurement. +SoilInterface heavy_metals overwrite_examples examples mercury 0.09 micrograms per gram|mercury 0.09 ug/g; chromium 0.03 ug/g +SoilInterface heavy_metals replace_attribute description Heavy metals present in the sample and their concentrations. +SoilInterface heavy_metals replace_attribute title heavy metals/ extreme unusual properties +SoilInterface heavy_metals_meth add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot +SoilInterface heavy_metals_meth overwrite_examples examples https://doi.org/10.3390/ijms9040434|mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8 +SoilInterface heavy_metals_meth replace_attribute title heavy metals method/ extreme unusual properties +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface horizon_meth replace_attribute title horizon method +PlantAssociatedInterface|SoilInterface humidity_regm replace_attribute recommended true +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface lat_lon add_attribute notes This is currently a required field but it's not clear if this should be required for human hosts AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface lat_lon replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface lat_lon replace_attribute string_serialization {lat lon} +PlantAssociatedInterface|SoilInterface light_regm replace_attribute recommended true +SoilInterface|WaterInterface organism_count replace_attribute pattern ^(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other)\|)*(\S+.*\S+;[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? \S+.*\S+;(qPCR|ATP|MPN|other))$ SoilInterface|WaterInterface organism_count replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface oxy_stat_samp add_attribute notes this is now a hybrid of the oxy_stat_samp semantics and the rel_to_oxygen enumeration AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface oxy_stat_samp replace_attribute range rel_to_oxygen_enum +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph add_attribute notes Use modified term +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute description pH measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute maximum_value 14 +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute minimum_value expects int?! 0 BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute range float +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute recommended true +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute string_serialization {float} +BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph_meth overwrite_examples examples https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB|https://doi.org/10.2136/sssabookser5.3.c16 AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface rel_to_oxygen replace_attribute range rel_to_oxygen_enum +SoilInterface salinity_meth overwrite_examples examples https://doi.org/10.1007/978-1-61779-986-0_28 +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_device add_attribute comments Report dimensions and details when applicable +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_device replace_attribute recommended true +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_method add_attribute comments This can be a citation or description +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface samp_mat_process overwrite_examples examples filtering of seawater|storing samples in ethanol AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface samp_mat_process replace_attribute range string +DhMultiviewCommonColumnsMixin samp_name add_attribute comments It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. +DhMultiviewCommonColumnsMixin samp_name overwrite_examples examples Rock core CB1178(5-6) from NSW +DhMultiviewCommonColumnsMixin samp_name replace_attribute description A local identifier or name that for the material sample collected. Refers to the original material collected or to any derived sub-samples. +DhMultiviewCommonColumnsMixin samp_name replace_attribute required true +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size add_attribute comments This refers to the TOTAL amount of sample collected from the experiment. NOT the amount sent to each institution or collected for a specific analysis. +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size overwrite_examples examples 5 grams|10 mL AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size replace_attribute range string +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size replace_attribute string_serialization {float} {unit} +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp overwrite_examples examples -80 Celsius +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp replace_attribute description Temperature at which the sample was stored (degrees are assumed) +AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp replace_attribute required true AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface sample_link replace_attribute range string AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface sample_link add_attribute notes "also tempted to include SampIdNewTermsMixin but if len(slot_usage.keys()) > 1 and ""placeholder"" in slot_usage.keys():AttributeError: 'list' object has no attribute 'keys'" -SoilInterface specific_ecosystem replace_attribute range SpecificEcosystemEnum -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface specific_ecosystem replace_attribute range string -SoilInterface store_cond replace_attribute range StoreCondEnum -BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content replace_attribute range string -PlantAssociatedInterface|SoilInterface air_temp_regm replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface alt replace_attribute recommended true -PlantAssociatedInterface|SoilInterface biotic_regm replace_attribute recommended true -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface chem_administration replace_attribute recommended true -PlantAssociatedInterface|SoilInterface climate_environment replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_category replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_subtype replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface ecosystem_type replace_attribute recommended true -PlantAssociatedInterface|SoilInterface gaseous_environment replace_attribute recommended true -PlantAssociatedInterface|SoilInterface humidity_regm replace_attribute recommended true -PlantAssociatedInterface|SoilInterface light_regm replace_attribute recommended true -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute recommended true -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_collec_device replace_attribute recommended true +SoilInterface season_precpt add_attribute notes mean and average are the same thing, but it seems like bad practice to not be consistent. Changed mean to average +SoilInterface season_precpt add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|check validation & examples. always mm? so value only? Or value + unit +SoilInterface season_precpt overwrite_examples examples 0.4 inch|10.16 mm +SoilInterface season_precpt replace_attribute title average seasonal precipitation +SoilInterface sieving add_attribute todos check validation and examples +SoilInterface sieving overwrite_examples examples combined 2 cores|4mm sieved|4 mm sieved and homogenized|50 g| 5 cores|2 mm sieved SoilInterface sieving replace_attribute recommended true SoilInterface size_frac_low replace_attribute recommended false SoilInterface size_frac_up replace_attribute recommended false -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface specific_ecosystem replace_attribute recommended true -PlantAssociatedInterface|SoilInterface watering_regm replace_attribute recommended true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_broad_scale replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_local_scale replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface env_medium replace_attribute required true -PlantAssociatedInterface|SoilInterface growth_facil replace_attribute required true -DhMultiviewCommonColumnsMixin samp_name replace_attribute required true -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_store_temp replace_attribute required true +SoilInterface slope_aspect add_attribute todos This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot +SoilInterface slope_aspect overwrite_examples examples 35 +SoilInterface slope_aspect replace_attribute description The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees). - This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration. +SoilInterface slope_gradient add_attribute todos Slope is a percent. How does the validation work? Check to correct examples +SoilInterface slope_gradient overwrite_examples examples 10%|10 %|0.1 +DhMultiviewCommonColumnsMixin source_mat_id add_attribute comments Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn), NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These IDs enable linking to derived analytes and subsamples. If you have not assigned FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/). +DhMultiviewCommonColumnsMixin source_mat_id add_attribute notes The source material IS the Globally Unique ID +DhMultiviewCommonColumnsMixin source_mat_id add_attribute todos Currently, the comments say to use UUIDs. However, if we implement assigning NMDC identifiers with the minter we dont need to require a GUID. It can be an optional field to fill out only if they already have a resolvable ID. +DhMultiviewCommonColumnsMixin source_mat_id overwrite_examples examples IGSN:AU1243|UUID:24f1467a-40f4-11ed-b878-0242ac120002 +DhMultiviewCommonColumnsMixin source_mat_id replace_attribute description A globally unique identifier assigned to the biological sample. +DhMultiviewCommonColumnsMixin source_mat_id replace_attribute identifier true DhMultiviewCommonColumnsMixin source_mat_id replace_attribute required true -SoilInterface store_cond replace_attribute required true -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface collection_date replace_attribute string_serialization {date, arbitrary precision} -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute string_serialization {float}|{float}-{float} -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface geo_loc_name replace_attribute string_serialization {text}: {text}, {text} -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface lat_lon replace_attribute string_serialization {lat lon} -BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|MiscEnvsInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface ph replace_attribute string_serialization {float} -AirInterface|BiofilmInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface samp_size replace_attribute string_serialization {float} {unit} DhMultiviewCommonColumnsMixin source_mat_id replace_attribute string_serialization {text}:{text} -SoilInterface al_sat replace_attribute title aluminum saturation/ extreme unusual properties -SoilInterface al_sat_meth replace_attribute title aluminum saturation method/ extreme unusual properties -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface depth replace_attribute title depth, meters -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface elev replace_attribute title elevation, meters -SoilInterface heavy_metals replace_attribute title heavy metals/ extreme unusual properties -SoilInterface heavy_metals_meth replace_attribute title heavy metals method/ extreme unusual properties -AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface horizon_meth replace_attribute title horizon method -SoilInterface season_precpt replace_attribute title average seasonal precipitation DhMultiviewCommonColumnsMixin source_mat_id replace_attribute title globally unique ID -SoilInterface extreme_event expected_value date, string -SoilInterface fire expected_value date string -SoilInterface flooding expected_value date string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface specific_ecosystem add_attribute notes string or SpecificEcosystemEnum range? +SoilInterface specific_ecosystem replace_attribute range SpecificEcosystemEnum +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|WastewaterSludgeInterface specific_ecosystem replace_attribute range string +AirInterface|BiofilmInterface|BuiltEnvInterface|HcrCoresInterface|HcrFluidsSwabsInterface|HostAssociatedInterface|MiscEnvsInterface|PlantAssociatedInterface|SedimentInterface|SoilInterface|WastewaterSludgeInterface|WaterInterface specific_ecosystem replace_attribute recommended true +SoilInterface store_cond replace_attribute description Explain how the soil sample is stored (fresh/frozen/other). +SoilInterface store_cond replace_attribute range StoreCondEnum +SoilInterface store_cond replace_attribute required true +BiofilmInterface|SedimentInterface|SoilInterface tot_carb add_attribute todos is this inorganic and organic? both? could use some clarification.|ug/L doesn't seem like the right units. Should check this slots usage in databases and re-evaluate. I couldn't find any references that provided this data in this format +BiofilmInterface|SedimentInterface|SoilInterface tot_carb overwrite_examples examples 1 ug/L +SoilInterface tot_nitro_cont_meth overwrite_examples examples https://doi.org/10.2134/agronmonogr9.2.c32|https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo +BiofilmInterface|SedimentInterface|SoilInterface tot_nitro_content overwrite_examples examples 5 mg N/ L +SoilInterface tot_org_c_meth overwrite_examples examples https://doi.org/10.1080/07352680902776556 +BiofilmInterface|SedimentInterface|SoilInterface tot_org_carb add_attribute todos check description. How are they different? +BiofilmInterface|SedimentInterface|SoilInterface tot_org_carb overwrite_examples examples 5 mg N/ L +SoilInterface water_cont_soil_meth add_attribute todos Why is it soil water content method in the name but not the title? Is this slot used in other samples?|Soil water content can be measure MANY ways and often, multiple ways are used in one experiment (gravimetric water content and water holding capacity and water filled pore space, to name a few).|Should this be multi valued? How to we manage and validate this? +SoilInterface water_cont_soil_meth overwrite_examples examples J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503|https://dec.alaska.gov/applications/spar/webcalc/definitions.htm +BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content add_attribute todos value in preferred unit is too limiting. need to change this|check and correct validation so examples are accepted|This is no longer matching the listed IRI from GSC. When NMDC has its own slots, map this to the MIxS slot|how to manage multiple water content methods? +BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content overwrite_examples examples 75%|75 %|0.75 g water/g dry soil|75% water holding capacity|1.1 g fresh weight/ dry weight|10% water filled pore space +BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content replace_attribute range string BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content expected_value string BiofilmInterface|SedimentInterface|SoilInterface|WaterInterface water_content preferred_unit gram per gram or cubic centimeter per cubic centimeter +PlantAssociatedInterface|SoilInterface watering_regm overwrite_examples examples 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M|75% water holding capacity; constant +PlantAssociatedInterface|SoilInterface watering_regm replace_attribute recommended true diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml index fbc3846c..7d6a2d33 100644 --- a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml +++ b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_type.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: bucket dna_cont_well: H3 diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml index 1173e5e0..46705905 100644 --- a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml +++ b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_cont_well.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: Z99 diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml index b814dd79..ff376146 100644 --- a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml +++ b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_dnase.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: C3 diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml index 2f8a0f37..e04587fe 100644 --- a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml +++ b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_sample_format.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: C3 diff --git a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml index 32785611..ddb83624 100644 --- a/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml +++ b/src/data/invalid/SampleData-jgi_mg_data-bad-dna_volume.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: C3 diff --git a/src/data/invalid/SampleData-jgi_mg_data-dna_collect_site.yaml b/src/data/invalid/SampleData-jgi_mg_data-dna_collect_site.yaml new file mode 100644 index 00000000..964e7244 --- /dev/null +++ b/src/data/invalid/SampleData-jgi_mg_data-dna_collect_site.yaml @@ -0,0 +1,23 @@ +jgi_mg_data: + - analysis_type: + - metagenomics + - metatranscriptomics + dna_collect_site: xxx + dna_concentration: 1.23 + dna_cont_type: plate + dna_cont_well: C3 + dna_container_id: xxx + dna_dnase: "no" + dna_isolate_meth: xxx + dna_project_contact: xxx + dna_samp_id: xxx + dna_sample_format: DNAStable + dna_sample_name: xxx + dna_seq_project: xxx + dna_seq_project_name: xxx + dna_seq_project_pi: xxx + dna_volume: 999 + proposal_dna: xxx + samp_name: xxx + source_mat_id: x:1 + diff --git a/src/data/invalid/SampleData-jgi_mg_data-dna_organisms.yaml b/src/data/invalid/SampleData-jgi_mg_data-dna_organisms.yaml new file mode 100644 index 00000000..f9c1edbe --- /dev/null +++ b/src/data/invalid/SampleData-jgi_mg_data-dna_organisms.yaml @@ -0,0 +1,22 @@ +jgi_mg_data: + - analysis_type: + - metagenomics + - metatranscriptomics + dna_concentration: 1.23 + dna_cont_type: plate + dna_cont_well: C3 + dna_container_id: xxx + dna_dnase: "no" + dna_isolate_meth: xxx + dna_project_contact: xxx + dna_samp_id: xxx + dna_sample_format: DNAStable + dna_sample_name: xxx + dna_seq_project: xxx + dna_seq_project_name: xxx + dna_seq_project_pi: xxx + dna_volume: 999 + proposal_dna: xxx + samp_name: xxx + source_mat_id: x:1 + dna_organisms: xxx diff --git a/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml b/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml index 3616b103..1f16f7e7 100644 --- a/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml +++ b/src/data/valid/SampleData-jgi_mg_data-exhaustive.yaml @@ -4,14 +4,14 @@ jgi_mg_data: - metatranscriptomics dna_absorb1: 1.23 dna_absorb2: 1.23 - dna_collect_site: xxx +# dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: C3 dna_container_id: xxx dna_dnase: "no" dna_isolate_meth: xxx - dna_organisms: xxx +# dna_organisms: xxx dna_project_contact: xxx dna_samp_id: xxx dna_sample_format: DNAStable diff --git a/src/data/valid/SampleData-jgi_mg_data-minimal.yaml b/src/data/valid/SampleData-jgi_mg_data-minimal.yaml index 964e7244..5026a363 100644 --- a/src/data/valid/SampleData-jgi_mg_data-minimal.yaml +++ b/src/data/valid/SampleData-jgi_mg_data-minimal.yaml @@ -2,7 +2,6 @@ jgi_mg_data: - analysis_type: - metagenomics - metatranscriptomics - dna_collect_site: xxx dna_concentration: 1.23 dna_cont_type: plate dna_cont_well: C3