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go-cam-shapes.shex
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go-cam-shapes.shex
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BASE <http://purl.obolibrary.org/obo/go/shapes/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX prov: <http://www.w3.org/ns/prov#>
#metadata
PREFIX bl: <https://w3id.org/biolink/vocab/>
PREFIX contributor: <http://purl.org/dc/elements/1.1/contributor>
PREFIX provided_by: <http://purl.org/pav/providedBy>
PREFIX modification_date: <http://purl.org/dc/elements/1.1/date>
PREFIX creation_date: <http://purl.org/dc/terms/created>
PREFIX import_date: <http://purl.org/dc/terms/dateAccepted>
PREFIX xref: <http://www.geneontology.org/formats/oboInOwl#hasDbXref>
PREFIX exact_match: <http://www.w3.org/2004/02/skos/core#exactMatch>
PREFIX source: <http://purl.org/dc/elements/1.1/source>
PREFIX evidence: <http://geneontology.org/lego/evidence>
PREFIX with: <http://geneontology.org/lego/evidence-with>
PREFIX x: <http://geneontology.org/lego/hint/layout/x>
PREFIX y: <http://geneontology.org/lego/hint/layout/y>
#model level annotations
PREFIX ontology: <http://www.w3.org/2002/07/owl#Ontology>
PREFIX taxon: <https://w3id.org/biolink/vocab/in_taxon>
PREFIX modelstate: <http://geneontology.org/lego/modelstate>
PREFIX templatestate: <http://geneontology.org/lego/templatestate>
PREFIX oboinowlid: <http://www.geneontology.org/formats/oboInOwl#id>
###contributor, date, providedBy reused
PREFIX title: <http://purl.org/dc/elements/1.1/title>
PREFIX imports: <http://www.w3.org/2002/07/owl#imports>
# always limit imports to? <http://purl.obolibrary.org/obo/go/extensions/go-lego.owl> ;
PREFIX in_taxon: <https://w3id.org/biolink/vocab/in_taxon>
#semantic: classes
PREFIX GoInformationBiomacromolecule: <http://purl.obolibrary.org/obo/CHEBI_33695>
PREFIX GoProtein: <http://purl.obolibrary.org/obo/CHEBI_36080>
PREFIX GoProteinContainingComplex: <http://purl.obolibrary.org/obo/GO_0032991>
PREFIX GoCellularComponent: <http://purl.obolibrary.org/obo/GO_0005575>
PREFIX GoBiologicalProcess: <http://purl.obolibrary.org/obo/GO_0008150>
PREFIX GoAnatomicalStructureDevelopment: <http://purl.obolibrary.org/obo/GO_0048856>
PREFIX GoAnatomicalStructureFormationInvolvedInMorphogenesis: <http://purl.obolibrary.org/obo/GO_0048646>
PREFIX GoAnatomicalStructureMorphogenesis: <http://purl.obolibrary.org/obo/GO_0009653>
PREFIX GoCellDifferentiation: <http://purl.obolibrary.org/obo/GO_0030154>
PREFIX GoCellDivision: <http://purl.obolibrary.org/obo/GO_0051301>
PREFIX GoCellFateCommitment: <http://purl.obolibrary.org/obo/GO_0045165>
PREFIX GoCellFateDetermination: <http://purl.obolibrary.org/obo/GO_0001709>
PREFIX GoCellFateSpecification: <http://purl.obolibrary.org/obo/GO_0001708>
PREFIX GoCellularComponentAssembly: <http://purl.obolibrary.org/obo/GO_0022607>
PREFIX GoCellularComponentDisassembly: <http://purl.obolibrary.org/obo/GO_0022411>
PREFIX GoCellularComponentOrganization: <http://purl.obolibrary.org/obo/GO_0016043>
PREFIX GoDevelopmentalMaturation: <http://purl.obolibrary.org/obo/GO_0021700>
PREFIX GoGrowth: <http://purl.obolibrary.org/obo/GO_0040007>
PREFIX GoLocalization: <http://purl.obolibrary.org/obo/GO_0051179>
PREFIX GoLocomotion: <http://purl.obolibrary.org/obo/GO_0040011>
PREFIX GoProteinContainingComplexRemodeling: <http://purl.obolibrary.org/obo/GO_0034367>
PREFIX GoPatternSpecificationProcess: <http://purl.obolibrary.org/obo/GO_0007389>
PREFIX GoMetabolicProcess: <http://purl.obolibrary.org/obo/GO_0008152>
PREFIX GoTransport: <http://purl.obolibrary.org/obo/GO_0006810>
PREFIX GoMolecularFunction: <http://purl.obolibrary.org/obo/GO_0003674>
prefix GoMolecularEvent: <http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event>
PREFIX GoTransporterActivity: <http://purl.obolibrary.org/obo/GO_0005215>
PREFIX GoChemicalEntity: <http://purl.obolibrary.org/obo/CHEBI_24431>
PREFIX GoEvidence: <http://purl.obolibrary.org/obo/ECO_0000000>
PREFIX GoAnatomicalEntity: <http://purl.obolibrary.org/obo/CARO_0000000>
PREFIX GoCell: <http://purl.obolibrary.org/obo/CL_0000000>
PREFIX GoOrganism: <http://purl.obolibrary.org/obo/NCBITaxon_1>
PREFIX GoBiologicalPhase: <http://purl.obolibrary.org/obo/GO_0044848>
PREFIX GoLifeCycleStage: <http://purl.obolibrary.org/obo/UBERON_0000105>
PREFIX GoPlantStructureDevelopmentStage: <http://purl.obolibrary.org/obo/PO_0009012>
#semantic: relations
PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050>
PREFIX has_part: <http://purl.obolibrary.org/obo/BFO_0000051>
PREFIX occurs_in: <http://purl.obolibrary.org/obo/BFO_0000066>
PREFIX adjacent_to: <http://purl.obolibrary.org/obo/RO_0002220>
PREFIX overlaps: <http://purl.obolibrary.org/obo/RO_0002131>
PREFIX existence_overlaps: <http://purl.obolibrary.org/obo/RO_0002490>
PREFIX existence_starts_and_ends_during: <http://purl.obolibrary.org/obo/RO_0002491>
PREFIX enabled_by: <http://purl.obolibrary.org/obo/RO_0002333>
PREFIX contributes_to: <http://purl.obolibrary.org/obo/RO_0002326>
PREFIX has_input: <http://purl.obolibrary.org/obo/RO_0002233>
PREFIX has_output: <http://purl.obolibrary.org/obo/RO_0002234>
PREFIX has_primary_input: <http://purl.obolibrary.org/obo/RO_0004009>
PREFIX has_primary_output: <http://purl.obolibrary.org/obo/RO_0004008>
PREFIX has_target_end_location: <http://purl.obolibrary.org/obo/RO_0002339>
PREFIX has_target_start_location: <http://purl.obolibrary.org/obo/RO_0002338>
PREFIX transports_or_maintains_localization_of: <http://purl.obolibrary.org/obo/RO_0002313>
PREFIX directly_provides_input_for: <http://purl.obolibrary.org/obo/RO_0002413>
PREFIX directly_positively_regulates: <http://purl.obolibrary.org/obo/RO_0002629>
PREFIX has_small_molecule_regulator: <http://purl.obolibrary.org/obo/RO_0012000>
PREFIX has_small_molecule_activator: <http://purl.obolibrary.org/obo/RO_0012001>
PREFIX has_small_molecule_inhibitor: <http://purl.obolibrary.org/obo/RO_0012002>
PREFIX is_small_molecule_regulator_of: <http://purl.obolibrary.org/obo/RO_0012004>
PREFIX is_small_molecule_activator_of: <http://purl.obolibrary.org/obo/RO_0012005>
PREFIX is_small_molecule_inhibitor_of: <http://purl.obolibrary.org/obo/RO_0012006>
PREFIX located_in: <http://purl.obolibrary.org/obo/RO_0001025>
PREFIX location_of: <http://purl.obolibrary.org/obo/RO_0001015>
PREFIX is_active_in: <http://purl.obolibrary.org/obo/RO_0002432>
PREFIX happens_during: <http://purl.obolibrary.org/obo/RO_0002092>
PREFIX regulates: <http://purl.obolibrary.org/obo/RO_0002211>
PREFIX negatively_regulates: <http://purl.obolibrary.org/obo/RO_0002212>
PREFIX positively_regulates: <http://purl.obolibrary.org/obo/RO_0002213>
PREFIX directly_regulates: <http://purl.obolibrary.org/obo/RO_0002578>
PREFIX directly_negatively_regulates: <http://purl.obolibrary.org/obo/RO_0002630>
PREFIX directly_activates: <http://purl.obolibrary.org/obo/RO_0002406>
PREFIX indirectly_regulates: <http://purl.obolibrary.org/obo/RO_0012012>
PREFIX indirectly_positively_regulates: <http://purl.obolibrary.org/obo/RO_0002407>
PREFIX indirectly_negatively_regulates: <http://purl.obolibrary.org/obo/RO_0002409>
PREFIX constitutively_upstream_of: <http://purl.obolibrary.org/obo/RO_0012009>
PREFIX removes_input_for: <http://purl.obolibrary.org/obo/RO_0012010>
PREFIX causally_upstream_of_or_within: <http://purl.obolibrary.org/obo/RO_0002418>
PREFIX causally_upstream_of_or_within_negative_effect: <http://purl.obolibrary.org/obo/RO_0004046>
PREFIX causally_upstream_of_or_within_positive_effect: <http://purl.obolibrary.org/obo/RO_0004047>
PREFIX causally_upstream_of: <http://purl.obolibrary.org/obo/RO_0002411>
PREFIX causally_upstream_of_negative_effect: <http://purl.obolibrary.org/obo/RO_0002305>
PREFIX causally_upstream_of_positive_effect: <http://purl.obolibrary.org/obo/RO_0002304>
PREFIX acts_on_population_of: <http://purl.obolibrary.org/obo/RO_0012003>
PREFIX results_in_development_of: <http://purl.obolibrary.org/obo/RO_0002296>
PREFIX results_in_formation_of: <http://purl.obolibrary.org/obo/RO_0002297>
PREFIX results_in_morphogenesis_of: <http://purl.obolibrary.org/obo/RO_0002298>
PREFIX results_in_acquisition_of_features_of: <http://purl.obolibrary.org/obo/RO_0002315>
PREFIX results_in_commitment_to: <http://purl.obolibrary.org/obo/RO_0002348>
PREFIX results_in_determination_of: <http://purl.obolibrary.org/obo/RO_0002349>
PREFIX results_in_specification_of: <http://purl.obolibrary.org/obo/RO_0002356>
PREFIX results_in_assembly_of: <http://purl.obolibrary.org/obo/RO_0002588>
PREFIX results_in_disassembly_of: <http://purl.obolibrary.org/obo/RO_0002590>
PREFIX results_in_organization_of: <http://purl.obolibrary.org/obo/RO_0002592>
PREFIX results_in_maturation_of: <http://purl.obolibrary.org/obo/RO_0002299>
PREFIX results_in_growth_of: <http://purl.obolibrary.org/obo/RO_0002343>
PREFIX results_in_movement_of: <http://purl.obolibrary.org/obo/RO_0002565>
PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
<GoCamModel> {
a [owl:Ontology] + ;
contributor: xsd:string +; #TODO would be better as an IRI
modification_date: xsd:string {1}; #Use ISO 8601 as a standard.
creation_date: xsd:string {0,1}; #Use ISO 8601 as a standard.
import_date: xsd:string {0,1}; #Use ISO 8601 as a standard.
provided_by: xsd:string +; #TODO would be better as an IRI
rdfs:comment xsd:string *;
modelstate: xsd:string {1}; #TODO would be better as an IRI
templatestate: xsd:string {0,1}; #TODO should be modeled as xsd:boolean but currently a string. No value means false.
in_taxon: . *;
title: xsd:string {1};
imports: . *;
oboinowlid: . *; #TODO not sure if we really want this?
owl:versionIRI . *;
prov:wasDerivedFrom IRI {0,1}; # for model copy
}
<ProvenanceAnnotated> {
contributor: xsd:string +; #TODO would be better as an IRI
modification_date: xsd:string {1}; #Use ISO 8601 as a standard.
creation_date: xsd:string {0,1}; #Use ISO 8601 as a standard.
import_date: xsd:string {0,1}; #Use ISO 8601 as a standard.
provided_by: xsd:string *; #TODO would be better as an IRI
rdfs:comment xsd:string *;
skos:note xsd:string *;
}
<GoCamEntity> IRI @<ProvenanceAnnotated> AND EXTRA a {
a [owl:NamedIndividual] * // rdfs:comment "Every entity we care about is a named individual";
xref: . * // rdfs:comment "mappings for the entity. Value is typically a CURIE string. Currently this is only used for Reactome-derived models." ;
rdfs:label . {0,1} // rdfs:comment "the name of the entity. Currently this is only used for Reactome-derived models." ;
exact_match: . *;
x: . {0,1} // rdfs:comment "X coordinate for node. This is used for caching layouts in the Noctua Graph Editor.";
y: . {0,1} // rdfs:comment "Y coordinate for node. This is used for caching layouts in the Noctua Graph Editor.";
skos:narrower . * // rdfs:comment "This entity (e.g. a node representing a pathway) represents a narrower (in any sense) concept then the target node. ";
skos:broader . * // rdfs:comment "This entity (e.g. a node representing a pathway) represents a broader (in any sense) concept then the target node. ";
} // rdfs:comment "Default allowable metadata for GO-CAM entities"
<OwlClass> {
rdf:type [ owl:Class ] {1};
}
<BiologicalProcessClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoBiologicalProcess: ] ;
}
<NegatedBiologicalProcessClass> BNode @<OwlClass> AND {
owl:complementOf @<BiologicalProcessClass>
}
<OrganismClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoOrganism: ] ;
}
<Organism> @<GoCamEntity> AND EXTRA a {
a @<OrganismClass> ;
} // rdfs:comment "A member of a class of organisms defined in the NCBI taxonomy"
<BiologicalProcess> @<GoCamEntity> AND EXTRA a {
a ( @<BiologicalProcessClass> OR @<NegatedBiologicalProcessClass> ) {1};
part_of: @<BiologicalProcess> *;
has_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
has_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_input: @<ChemicalEntity> *;
has_primary_output: @<ChemicalEntity> *;
occurs_in: @<AnatomicalEntity> {0,1};
transports_or_maintains_localization_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
has_target_end_location: @<AnatomicalEntity> {0,1};
has_target_start_location: @<AnatomicalEntity> {0,1};
causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
regulates: @<BiologicalProcess> *;
negatively_regulates: @<BiologicalProcess> *;
positively_regulates: @<BiologicalProcess> *;
acts_on_population_of: ( @<AnatomicalEntity> OR @<Organism> ) *;
happens_during: ( @<BiologicalPhase> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
} // rdfs:comment "A biological process"
<AnatomicalStructureDevelopmentClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoAnatomicalStructureDevelopment: ] ;
}
<AnatomicalStructureDevelopment> @<BiologicalProcess> AND EXTRA a {
a @<AnatomicalStructureDevelopmentClass> {1};
results_in_development_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "an anatomical structure development class GO biological process or child"
<AnatomicalStructureFormationInvolvedInMorphogenesisClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoAnatomicalStructureFormationInvolvedInMorphogenesis: ] ;
}
<AnatomicalStructureFormationInvolvedInMorphogenesis> @<BiologicalProcess> AND EXTRA a {
a @<AnatomicalStructureFormationInvolvedInMorphogenesisClass> {1};
results_in_formation_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "an anatomical structure formation involved in morphogenesis class GO biological process or child"
<AnatomicalStructureMorphogenesisClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoAnatomicalStructureMorphogenesis: ] ;
}
<AnatomicalStructureMorphogenesis> @<BiologicalProcess> AND EXTRA a {
a @<AnatomicalStructureMorphogenesisClass> {1};
results_in_morphogenesis_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "an anatomical structure morphogenesis class GO biological process or child"
<CellDifferentiationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellDifferentiation: ] ;
}
<CellDifferentiation> @<BiologicalProcess> AND EXTRA a {
a @<CellDifferentiationClass> {1};
results_in_acquisition_of_features_of: @<Cell> {0,1};
} // rdfs:comment "a cell differentiation GO biological process or child"
<CellDivisionClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellDivision: ] ;
}
<CellDivision> @<BiologicalProcess> AND EXTRA a {
a @<CellDivisionClass> {1};
has_input: @<Cell> {0,1};
} // rdfs:comment "a cell division GO biological process or child"
<CellFateCommitmentClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellFateCommitment: ] ;
}
<CellFateCommitment> @<BiologicalProcess> AND EXTRA a {
a @<CellFateCommitmentClass> {1};
results_in_commitment_to: @<Cell> {0,1};
} // rdfs:comment "a cell fate commitment GO biological process or child"
<CellFateDeterminationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellFateDetermination: ] ;
}
<CellFateDetermination> @<BiologicalProcess> AND EXTRA a {
a @<CellFateDeterminationClass> {1};
results_in_determination_of: @<Cell> {0,1};
} // rdfs:comment "a cell fate determination GO biological process or child"
<CellFateSpecificationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellFateSpecification: ] ;
}
<CellFateSpecification> @<BiologicalProcess> AND EXTRA a {
a @<CellFateSpecificationClass> {1};
results_in_specification_of: @<Cell> {0,1};
} // rdfs:comment "a cell fate specification GO biological process or child"
<CellularComponentAssemblyClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellularComponentAssembly: ] ;
}
<CellularComponentAssembly> @<BiologicalProcess> AND EXTRA a {
a @<CellularComponentAssemblyClass> {1};
results_in_assembly_of: @<CellularComponent> {0,1};
} // rdfs:comment "a cellular component assembly GO biological process or child"
<CellularComponentDisassemblyClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellularComponentDisassembly: ] ;
}
<CellularComponentDisassembly> @<BiologicalProcess> AND EXTRA a {
a @<CellularComponentDisassemblyClass> {1};
results_in_disassembly_of: @<CellularComponent> {0,1};
} // rdfs:comment "a cellular component disassembly GO biological process or child"
<CellularComponentOrganizationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellularComponentOrganization: ] ;
}
<CellularComponentOrganization> @<BiologicalProcess> AND EXTRA a {
a @<CellularComponentOrganizationClass> {1};
results_in_organization_of: @<CellularComponent> {0,1};
} // rdfs:comment "a cellular component organization GO biological process or child"
<DevelopmentalMaturationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoDevelopmentalMaturation: ] ;
}
<DevelopmentalMaturation> @<BiologicalProcess> AND EXTRA a {
a @<DevelopmentalMaturationClass> {1};
results_in_maturation_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a developmental maturation GO biological process or child"
<GrowthClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoGrowth: ] ;
}
<Growth> @<BiologicalProcess> AND EXTRA a {
a @<GrowthClass> {1};
results_in_growth_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a growth GO biological process or child"
<LocalizationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoLocalization: ] ;
}
<Localization> @<BiologicalProcess> AND EXTRA a {
a @<LocalizationClass> {1};
transports_or_maintains_localization_of: ( @<AnatomicalEntity> OR @<ChemicalEntity> OR @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
has_target_end_location: @<AnatomicalEntity> {0,1};
has_target_start_location: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a localization GO biological process or child"
<LocomotionClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoLocomotion: ] ;
}
<Locomotion> @<BiologicalProcess> AND EXTRA a {
a @<LocomotionClass> {1};
results_in_movement_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a locomotion GO biological process or child"
<MetabolicProcessClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoMetabolicProcess: ] ;
}
<MetabolicProcess> @<BiologicalProcess> AND EXTRA a {
a @<MetabolicProcessClass> {1};
has_primary_input: @<ChemicalEntity> *;
has_primary_output: @<ChemicalEntity> *;
} // rdfs:comment "a metabolic process GO biological process or child"
<ProteinContainingComplexRemodelingClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoProteinContainingComplexRemodeling: ] ;
}
<ProteinContainingComplexRemodeling> @<BiologicalProcess> AND EXTRA a {
a @<ProteinContainingComplexRemodelingClass> {1};
results_in_remodeling_of: @<ProteinContainingComplex> {0,1};
} // rdfs:comment "a protein containing complex remodeling GO biological process or child"
<PatternSpecificationProcessClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoPatternSpecificationProcess: ] ;
}
<PatternSpecificationProcess> @<BiologicalProcess> AND EXTRA a {
a @<PatternSpecificationProcessClass> {1};
results_in_specification_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a pattern specification process GO biological process or child"
<TransportClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoTransport: ] ;
}
<Transport> @<BiologicalProcess> AND EXTRA a {
a @<TransportClass> {1};
has_primary_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
} // rdfs:comment "a transport GO biological process or child"
<MolecularFunctionClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoMolecularFunction: ] ;
}
<NegatedMolecularFunctionClass> BNode @<OwlClass> AND {
owl:complementOf @<MolecularFunctionClass>
}
<MolecularEventClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoMolecularEvent: ] ;
}
<NegatedMolecularEventClass> BNode @<OwlClass> AND {
owl:complementOf @<MolecularEventClass>
}
<MolecularEvent> @<GoCamEntity> AND EXTRA a {
a ( @<MolecularEventClass> OR @<NegatedMolecularEventClass> ) {1};
}
<MolecularFunction> @<GoCamEntity> AND EXTRA a {
a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
enabled_by: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
part_of: @<BiologicalProcess> *;
has_part: @<MolecularFunction> *;
occurs_in: @<AnatomicalEntity> {0,1};
has_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
directly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
indirectly_regulates: ( @<MolecularFunction> OR @<MolecularEvent>) *;
indirectly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
indirectly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
constitutively_upstream_of: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
removes_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
has_small_molecule_regulator: @<ChemicalEntity> *;
has_small_molecule_activator: @<ChemicalEntity> *;
has_small_molecule_inhibitor: @<ChemicalEntity> *;
causally_upstream_of_or_within: ( @<MolecularFunction> OR @<MolecularEvent> OR @<BiologicalProcess> ) *;
causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> *;
causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> *;
causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
happens_during: ( @<BiologicalPhase> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
} // rdfs:comment "A molecular function"
<TransporterActivityClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoTransporterActivity: ];
}
<TransporterActivity> @<MolecularFunction> AND EXTRA a {
a @<TransporterActivityClass> {1};
transports_or_maintains_localization_of: ( @<ChemicalEntity> OR @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
has_primary_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_primary_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
has_target_end_location: @<CellularComponent> *;
has_target_start_location: @<CellularComponent> *;
} // rdfs:comment "a transporter activity GO molecular function or child"
<BiologicalPhaseClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoBiologicalPhase: ];
}
<BiologicalPhase> @<GoCamEntity> AND EXTRA a {
a @<BiologicalPhaseClass>;
} // rdfs:comment "a biological phase"
<LifeCycleStageClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoLifeCycleStage: ];
}
<LifeCycleStage> @<GoCamEntity> AND EXTRA a {
a @<LifeCycleStageClass>;
} // rdfs:comment "a lifecycle stage"
<PlantStructureDevelopmentStageClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoPlantStructureDevelopmentStage: ];
}
<PlantStructureDevelopmentStage> @<GoCamEntity> AND EXTRA a {
a @<PlantStructureDevelopmentStageClass>;
} // rdfs:comment "a plant structure developmental stage"
<AnatomicalEntityClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoAnatomicalEntity: ];
}
<NegatedAnatomicalEntityClass> BNode @<OwlClass> AND {
owl:complementOf @<AnatomicalEntityClass>
}
<AnatomicalEntity> @<GoCamEntity> AND EXTRA a {
a ( @<AnatomicalEntityClass> OR @<NegatedAnatomicalEntityClass> );
part_of: @<AnatomicalEntity> {0,1};
location_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {0,1};
} // rdfs:comment "an anatomical entity"
<CellClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCell: ];
}
<Cell> @<GoCamEntity> AND EXTRA a {
a @<CellClass> {1};
part_of: @<AnatomicalEntity> {0,1};
} // rdfs:comment "a cell or child"
<CellularComponentClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoCellularComponent: ];
}
<NegatedCellularComponentClass> BNode @<OwlClass> AND {
owl:complementOf @<CellularComponentClass>
}
<RootCellularComponent> IRI @<GoCamEntity> AND EXTRA a {
a [ GoCellularComponent: ];
}
#<CellularComponent> @<AnatomicalEntity> AND EXTRA a { # If we want to intersect with anatomical entity, then GO cellular_component needs to subclass anatomical entity in go-lego
<CellularComponent> @<GoCamEntity> AND EXTRA a {
a ( @<CellularComponentClass> OR @<NegatedCellularComponentClass> ) {1};
part_of: @<AnatomicalEntity> {0,1};
adjacent_to: @<AnatomicalEntity> *;
overlaps: @<AnatomicalEntity> *;
existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
} // rdfs:comment "a cellular component"
<ProteinContainingComplex> @<GoCamEntity> AND EXTRA a {
a @<ProteinContainingComplexClass>;
located_in: @<AnatomicalEntity> {0,1};
is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1};
has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex>) *;
existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
} // rdfs:comment "a protein complex"
<ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoProteinContainingComplex: ];
}
<ChemicalEntity> @<GoCamEntity> AND EXTRA a {
a @<ChemicalEntityClass> +;
is_small_molecule_regulator_of: @<MolecularFunction> *;
is_small_molecule_activator_of: @<MolecularFunction> *;
is_small_molecule_inhibitor_of: @<MolecularFunction> *;
}// rdfs:comment "a molecular entity (a gene product, chemical, or complex typically)"
<ChemicalEntityClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoChemicalEntity: ];
}
<ProteinClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoProtein: ];
}
<Protein> @<ChemicalEntity> AND EXTRA a {
a @<ProteinClass> ;
located_in: @<AnatomicalEntity> {0,1};
is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1};
part_of: @<ProteinContainingComplex> {0,1};
contributes_to: @<MolecularFunction> {0,1};
}// rdfs:comment "a protein"
<InformationBiomacromoleculeClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoInformationBiomacromolecule: ];
}
<InformationBiomacromolecule> @<ChemicalEntity> AND EXTRA a {
a @<InformationBiomacromoleculeClass> +;
located_in: @<AnatomicalEntity> {0,1};
is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1};
part_of: @<ProteinContainingComplex> {0,1};
contributes_to: @<MolecularFunction> {0,1};
}// rdfs:comment "an information biomacromolecule - e.g. a protein or RNA product"
<EvidenceClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
rdfs:subClassOf [ GoEvidence: ] ;
}
<Evidence> @<GoCamEntity> AND EXTRA a {
a @<EvidenceClass> {1};
source: xsd:string {1};
with: xsd:string {0,1}
}// rdfs:comment "A kind of evidence"
<AnnotatedEdge> BNode @<ProvenanceAnnotated> AND {
a [ owl:Axiom ] ;
owl:annotatedSource @<GoCamEntity> ;
owl:annotatedProperty IRI ;
owl:annotatedTarget @<GoCamEntity> ;
evidence: @<Evidence> *
}
#<BL_UNTYPED> {
# bl:category . {0}
# // rdfs:comment "has no type tag inside" ;
#} // rdfs:comment "has no type tag full rule"
#<BL_TYPED> {
# bl:category . {1}
#} // rdfs:comment "has exactly one type tag"
#<BL_MULTI_TYPED> {
# bl:category . {2,}
#} // rdfs:comment "has multiple type tags"