PREFIX gocam:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
gocam:MoleculeAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a molecule node" ;
rdfs:subClassOf gocam:Association .
gocam:predicate a rdf:Property ;
rdfs:comment "The RO relation that represents the type of relationship" ;
rdfs:range gocam:PredicateTermObject .
gocam:provenances a rdf:Property ;
rdfs:comment "The set of provenance objects that provide metadata about who made the association." , "Model-level provenance information" , "Provenance information for the activity" , "Provenance about the assertion, e.g. who made it" ;
rdfs:range gocam:ProvenanceInfo .
gocam:molecule a rdf:Property ;
rdfs:comment "The molecule node that is associated with this activity" ;
rdfs:range gocam:MoleculeNode .
gocam:evidence a rdf:Property ;
rdfs:comment "The set of evidence items that support the association." ;
rdfs:range gocam:EvidenceItem .
gocam:type a rdf:Property ;
rdfs:comment "The type of association." ;
rdfs:range xsd:string , xsd:anyURI .
gocam:EnabledByProteinComplexAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a protein complex, where the complex carries out the activity. This should only be used when the activity cannot be attributed to an individual member of the complex, but instead the function is an emergent property of the complex." ;
rdfs:subClassOf gocam:EnabledByAssociation .
gocam:term a rdf:Property ;
rdfs:comment "The gene product or complex that carries out the activity" , "The phase ontology term associated with the biological process (not the relation type)" , "The ontology term that describes the nature of the association" , "The molecule term associated with the molecule node" , "The protein complex that the gene product is a part of." , "The gene product that is part of the protein complex." , "A \"term\" that is an entity database object representing an individual gene product." , "The ECO term representing the type of evidence" ;
rdfs:range gocam:ProteinComplexTermObject , gocam:PhaseTermObject , gocam:BiologicalProcessTermObject , gocam:GrossAnatomicalStructureTermObject , gocam:MoleculeTermObject , gocam:InformationBiomacromoleculeTermObject , gocam:GeneProductTermObject , gocam:CellularAnatomicalEntityTermObject , gocam:TermObject , gocam:MolecularFunctionTermObject , gocam:CellTypeTermObject , gocam:EvidenceTermObject .
gocam:has_part a rdf:Property ;
rdfs:comment "Associations between the complex and gene products that are part of it." ;
rdfs:range gocam:ProteinComplexHasPartAssociation .
gocam:PhaseAssociation a rdfs:Class ;
rdfs:comment "An association between an activity or biological process and a phase term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:PredicateTermObject a rdfs:Class ;
rdfs:comment "A term object that represents an OWL relation from the OBO Relations Ontology" ;
rdfs:subClassOf gocam:TermObject .
rdfs:label a rdf:Property ;
rdfs:range xsd:string .
gocam:obsolete a rdf:Property ;
rdfs:range xsd:boolean .
gocam:BiologicalProcessAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a biological process term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:happens_during a rdf:Property ;
rdfs:comment "Optional extension describing the phase during which the BP takes place" , "The phase during which the activity takes place" ;
rdfs:range gocam:PhaseAssociation .
gocam:part_of a rdf:Property ;
rdfs:comment "Optional extension allowing hierarchical nesting of BPs" , "Associations between the gene product and protein complexes it is a part of." , "Optional extension allowing hierarchical nesting of CCs" , "The larger biological process in which the activity is a part" ;
rdfs:range gocam:BiologicalProcessAssociation , gocam:GrossAnatomyAssociation , gocam:PartOfProteinComplexAssociation , gocam:CellTypeAssociation .
gocam:ProvenanceInfo a rdfs:Class ;
rdfs:comment "Provenance information for an object" .
a rdf:Property ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:comment "The date that the model was last modified" ;
rdfs:range xsd:string .
a rdf:Property ;
rdfs:range xsd:string .
gocam:GrossAnatomyAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a gross anatomical structure term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:MoleculeNode a rdfs:Class ;
rdfs:comment "An individual molecule or chemical entity in a causal model, representing a specific occurrence of a molecule that participates in activities as an input or output and may be localized to a particular cellular location." .
gocam:located_in a rdf:Property ;
rdfs:comment "The cellular location in which the molecule is located" ;
rdfs:range gocam:CellularAnatomicalEntityAssociation .
gocam:PartOfProteinComplexAssociation a rdfs:Class ;
rdfs:comment "An association between a gene product and a protein complex that it is a part of." ;
rdfs:subClassOf gocam:TermAssociation .
gocam:TaxonTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a taxon term from NCBITaxon" ;
rdfs:subClassOf gocam:TermObject .
gocam:ProteinComplexTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a protein complex term from GO" ;
rdfs:subClassOf gocam:InformationBiomacromoleculeTermObject .
gocam:MoleculeTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a molecule term from CHEBI or UniProtKB" ;
rdfs:subClassOf gocam:TermObject .
gocam:EnabledByAssociation a rdfs:Class ;
rdfs:comment """An association between an activity and the gene product or complex or set of potential gene products
that carry out that activity.""" ;
rdfs:subClassOf gocam:Association .
gocam:CellularAnatomicalEntityTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a cellular anatomical entity term from GO" ;
rdfs:subClassOf gocam:TermObject .
gocam:PublicationObject a rdfs:Class ;
rdfs:comment "An object that represents a publication or other kind of reference" ;
rdfs:subClassOf gocam:Object .
gocam:abstract_text a rdf:Property ;
rdfs:range xsd:string .
gocam:full_text a rdf:Property ;
rdfs:range xsd:string .
gocam:CausalAssociation a rdfs:Class ;
rdfs:comment "A causal association between two activities" ;
rdfs:subClassOf gocam:Association .
gocam:downstream_activity a rdf:Property ;
rdfs:comment "The activity unit that is downstream of this one" ;
rdfs:range gocam:Activity .
gocam:EvidenceTermObject a rdfs:Class ;
rdfs:comment "A term object that represents an evidence term from ECO. Only ECO terms that map up to a GO GAF evidence code should be used." ;
rdfs:subClassOf gocam:TermObject .
gocam:ProteinComplexHasPartAssociation a rdfs:Class ;
rdfs:comment "An association between a protein complex and one of its parts." ;
rdfs:subClassOf gocam:TermAssociation .
gocam:CellularAnatomicalEntityAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a cellular anatomical entity term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:EnabledByGeneProductAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and an individual gene product" ;
rdfs:subClassOf gocam:EnabledByAssociation .
gocam:MolecularFunctionTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a molecular function term from GO" ;
rdfs:subClassOf gocam:TermObject .
gocam:Model a rdfs:Class ;
rdfs:comment "A model of a biological program consisting of a set of causally connected activities." .
gocam:activities a rdf:Property ;
rdfs:comment "All of the activities that are part of the model" ;
rdfs:range gocam:Activity .
a rdf:Property ;
rdfs:comment "The status of the model in terms of its progression along the developmental lifecycle" ;
rdfs:range gocam:ModelStateEnum .
gocam:taxon a rdf:Property ;
rdfs:comment "The primary taxon that the model is about" ;
rdfs:range gocam:TaxonTermObject .
rdfs:comment a rdf:Property ;
rdfs:comment "Curator-provided comments about the model" ;
rdfs:range xsd:string .
gocam:query_index a rdf:Property ;
rdfs:comment "An optional object that contains the results of indexing a model with various summary statistics and retrieval indices." ;
rdfs:range gocam:QueryIndex .
gocam:additional_taxa a rdf:Property ;
rdfs:comment "Additional taxa that the model is about" ;
rdfs:range gocam:TaxonTermObject .
gocam:molecules a rdf:Property ;
rdfs:comment "All of the molecule nodes that are part of the model." ;
rdfs:range gocam:MoleculeNode .
a rdf:Property ;
rdfs:comment "The human-readable descriptive title of the model" ;
rdfs:range xsd:string .
gocam:objects a rdf:Property ;
rdfs:comment "All of the objects that are part of the model. This includes terms as well as publications and database objects like gene. This is not strictly part of the data managed by the model, it is for convenience, and should be refreshed from outside." ;
rdfs:range gocam:Object .
gocam:GeneProductTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a gene product term from GO or UniProtKB" ;
rdfs:subClassOf gocam:InformationBiomacromoleculeTermObject .
gocam:Activity a rdfs:Class ;
rdfs:comment "An individual activity in a causal model, representing the individual molecular activity of a single gene product or complex in the context of a particular model" .
gocam:occurs_in a rdf:Property ;
rdfs:comment "The cellular location in which the activity occurs" ;
rdfs:range gocam:CellularAnatomicalEntityAssociation .
gocam:molecular_associations a rdf:Property ;
rdfs:comment "Associations between the activity and molecules that are relevant to it. This includes molecules that are products/substrates or regulators of the activity." ;
rdfs:range gocam:MoleculeAssociation .
gocam:enabled_by a rdf:Property ;
rdfs:comment "The gene product or complex that carries out the activity" ;
rdfs:range gocam:EnabledByAssociation .
gocam:molecular_function a rdf:Property ;
rdfs:comment "The molecular function that is carried out by the gene product or complex" ;
rdfs:range gocam:MolecularFunctionAssociation .
gocam:causal_associations a rdf:Property ;
rdfs:comment "The causal associations that flow out of this activity" ;
rdfs:range gocam:CausalAssociation .
gocam:TermAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a term, potentially with extensions. This is an abstract class for grouping purposes, it should not be directly instantiated, instead a subclass should be instantiated." ;
rdfs:subClassOf gocam:Association .
gocam:QueryIndex a rdfs:Class ;
rdfs:comment "An index that is optionally placed on a model in order to support common query or index operations. Note that this index is not typically populated in the working transactional store for a model, it is derived via computation from core primary model information." .
gocam:model_activity_enabled_by_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of `model_activity_enabled_by_terms`, over the is_a and part_of relationship types" ;
rdfs:range gocam:TermObject .
gocam:model_activity_has_input_terms a rdf:Property ;
rdfs:comment "All direct input terms for all activities" ;
rdfs:range gocam:TermObject .
gocam:model_activity_molecular_function_terms a rdf:Property ;
rdfs:comment "All MF terms for all activities" ;
rdfs:range gocam:TermObject .
gocam:model_taxon_rollup a rdf:Property ;
rdfs:comment "The rollup of the taxon closure to a NCBITaxon subset or slim." ;
rdfs:range gocam:TermObject .
gocam:intermediate_activities a rdf:Property ;
rdfs:comment "The set of activities that are neither start nor end activities, i.e. those that have both incoming and outgoing causal associations." ;
rdfs:range gocam:Activity .
gocam:number_of_start_activities a rdf:Property ;
rdfs:comment "The number of start activities in a model" ;
rdfs:range xsd:integer .
gocam:model_activity_has_input_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of `model_activity_has_input_terms`, over the is_a relationship type" ;
rdfs:range gocam:TermObject .
gocam:flattened_contributors a rdf:Property ;
rdfs:comment "All contributor values from the model across different levels combined in one place" ;
rdfs:range xsd:string .
gocam:end_activities a rdf:Property ;
rdfs:comment "The set of activities that are the end points of the model, i.e. those that have no outgoing causal associations." ;
rdfs:range gocam:Activity .
gocam:flattened_references a rdf:Property ;
rdfs:comment "All publication objects from the model across different levels combined in one place" ;
rdfs:range gocam:PublicationObject .
gocam:model_activity_enabled_by_terms a rdf:Property ;
rdfs:comment "All direct enabler terms for all activities" ;
rdfs:range gocam:TermObject .
gocam:model_activity_has_input_rollup a rdf:Property ;
rdfs:comment "The rollup of `model_activity_has_input_closure` to a GO subset or slim." ;
rdfs:range gocam:TermObject .
gocam:model_activity_enabled_by_genes a rdf:Property ;
rdfs:comment "All direct enabler genes and genes that are part of enabler complexes for all activities" ;
rdfs:range gocam:TermObject .
gocam:number_of_end_activities a rdf:Property ;
rdfs:comment "The number of end activities in a model" ;
rdfs:range xsd:integer .
gocam:model_activity_occurs_in_terms a rdf:Property ;
rdfs:comment "All direct cellular component localization terms for all activities" ;
rdfs:range gocam:TermObject .
gocam:annoton_terms a rdf:Property ;
rdfs:range gocam:TermObject .
gocam:model_activity_molecular_function_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of `model_activity_molecular_function_terms`, over the is_a relationship" ;
rdfs:range gocam:TermObject .
gocam:flattened_evidence_terms a rdf:Property ;
rdfs:comment "All evidence term objects from the model across different levels combined in one place" ;
rdfs:range gocam:EvidenceTermObject .
gocam:number_of_intermediate_activities a rdf:Property ;
rdfs:comment "The number of intermediate activities in a model" ;
rdfs:range xsd:integer .
gocam:singleton_activities a rdf:Property ;
rdfs:comment "The set of activities that have no causal associations, i.e. those that are not connected to any other activity in the model." ;
rdfs:range gocam:Activity .
gocam:taxon_label a rdf:Property ;
rdfs:comment "The label of the primary taxon for the model" ;
rdfs:range xsd:string .
gocam:number_of_causal_associations a rdf:Property ;
rdfs:comment "Total number of causal association edges connecting activities in a model. This includes both explicit causal associations (e.g. \"directly positively regulates\") between activities and implicit causal associations between activities with shared input/output chemical entities." ;
rdfs:range xsd:integer .
gocam:model_activity_part_of_rollup a rdf:Property ;
rdfs:comment "The rollup of `model_activity_part_of_closure` to a GO subset or slim." ;
rdfs:range gocam:TermObject .
gocam:model_activity_occurs_in_rollup a rdf:Property ;
rdfs:comment "The rollup of `model_activity_occurs_in_closure` to a GO subset or slim." ;
rdfs:range gocam:TermObject .
gocam:model_activity_part_of_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of `model_activity_part_of_terms`, over the is_a and part_of relationship type" ;
rdfs:range gocam:TermObject .
gocam:model_activity_occurs_in_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of `model_activity_occurs_in_terms`, over the is_a and part_of relationship type" ;
rdfs:range gocam:TermObject .
gocam:model_activity_enabled_by_rollup a rdf:Property ;
rdfs:comment "The rollup of `model_activity_enabled_by_closure` to a GO subset or slim." ;
rdfs:range gocam:TermObject .
gocam:number_of_singleton_activities a rdf:Property ;
rdfs:comment "The number of singleton activities in a model" ;
rdfs:range xsd:integer .
gocam:model_taxon a rdf:Property ;
rdfs:comment "The primary taxon term for the model, over the NCBITaxon:subClassOf relationship type. This is used to determine the primary taxon that the model is relevant to." ;
rdfs:range gocam:TermObject .
gocam:model_activity_part_of_terms a rdf:Property ;
rdfs:comment "All direct biological process terms for all activities" ;
rdfs:range gocam:TermObject .
gocam:model_taxon_closure a rdf:Property ;
rdfs:comment "The reflexive transitive closure of the taxon term for the model, over the NCBITaxon:subClassOf relationship type. This is used to determine the set of taxa that are relevant to the model." ;
rdfs:range gocam:TermObject .
gocam:number_of_strongly_connected_components a rdf:Property ;
rdfs:comment "The number of distinct components that consist of activities that are connected (directly or indirectly) via causal connections. Most models will consist of a single SCC. Some models may consist of two or more \"islands\" where there is no connection from one island to another." ;
rdfs:range xsd:integer .
gocam:start_activities a rdf:Property ;
rdfs:comment "The set of activities that are the starting points of the model, i.e. those that have no incoming causal associations." ;
rdfs:range gocam:Activity .
gocam:number_of_activities a rdf:Property ;
rdfs:comment "The number of activities in a model." ;
rdfs:range xsd:integer .
gocam:number_of_enabled_by_terms a rdf:Property ;
rdfs:comment "The number of molecular entities or sets of entities in a model." ;
rdfs:range xsd:integer .
gocam:model_activity_molecular_function_rollup a rdf:Property ;
rdfs:comment "The rollup of `model_activity_molecular_function_closure` to a GO subset or slim." ;
rdfs:range gocam:TermObject .
gocam:flattened_provided_by a rdf:Property ;
rdfs:comment "All provided_by values from the model across different levels combined in one place" ;
rdfs:range gocam:Object .
gocam:model_chemical_terms a rdf:Property ;
rdfs:comment "All molecule terms in the model that are chemical entities (e.g. substrates or products) and not information biomacromolecules (e.g. gene products or complexes)." ;
rdfs:range gocam:TermObject .
gocam:length_of_longest_causal_association_path a rdf:Property ;
rdfs:comment "The maximum number of hops along activities along the direction of causal flow in a model." ;
rdfs:range xsd:integer .
gocam:Association a rdfs:Class ;
rdfs:comment "An abstract grouping for different kinds of evidence-associated provenance" .
gocam:Object a rdfs:Class ;
rdfs:comment "An abstract class for all identified objects in a model" .
gocam:GrossAnatomicalStructureTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a gross anatomical structure term from UBERON" ;
rdfs:subClassOf gocam:TermObject .
gocam:MolecularFunctionAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a molecular function term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:BiologicalProcessTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a biological process term from GO" ;
rdfs:subClassOf gocam:TermObject .
gocam:InformationBiomacromoleculeTermObject a rdfs:Class ;
rdfs:comment "An abstract class for all information biomacromolecule term objects" ;
rdfs:subClassOf gocam:TermObject .
gocam:PhaseTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a phase term from GO or UBERON" ;
rdfs:subClassOf gocam:TermObject .
gocam:CellTypeAssociation a rdfs:Class ;
rdfs:comment "An association between an activity and a cell type term" ;
rdfs:subClassOf gocam:TermAssociation .
gocam:TermObject a rdfs:Class ;
rdfs:comment "An abstract class for all ontology term objects" ;
rdfs:subClassOf gocam:Object .
gocam:EvidenceItem a rdfs:Class ;
rdfs:comment "An individual piece of evidence that is associated with an assertion in a model" .
gocam:reference a rdf:Property ;
rdfs:comment "The publication of reference that describes the evidence" ;
rdfs:range gocam:PublicationObject .
gocam:with_objects a rdf:Property ;
rdfs:comment "Supporting database entities or terms" ;
rdfs:range gocam:Object .
gocam:CellTypeTermObject a rdfs:Class ;
rdfs:comment "A term object that represents a cell type term from CL" ;
rdfs:subClassOf gocam:TermObject .
gocam:ModelStateEnum a rdfs:Class ;
rdfs:comment "A term describing where the model is in the development life cycle." .
gocam:ModelStateEnum.DEVELOPMENT a gocam:ModelStateEnum ;
rdfs:comment "Used when the curator is still working on the model. Edits are still being made, and the information in the model is not yet guaranteed to be accurate or complete. The model should not be displayed in end-user facing websites, unless it is made clear that the model is a work in progress." .
gocam:ModelStateEnum.PRODUCTION a gocam:ModelStateEnum ;
rdfs:comment "Used when the curator has declared the model is ready for public consumption. Edits might still be performed on the model in future, but the information in the model is believed to be both accurate and reasonably complete. The model may be displayed in public websites." .
gocam:ModelStateEnum.DELETE a gocam:ModelStateEnum ;
rdfs:comment "When the curator has marked for future deletion." .
gocam:ModelStateEnum.REVIEW a gocam:ModelStateEnum ;
rdfs:comment "The model has been marked for curator review." .
gocam:ModelStateEnum.INTERNAL_TEST a gocam:ModelStateEnum ;
rdfs:comment "The model is not intended for use public use; it is likely to be used for internal testing." .
gocam:ModelStateEnum.TEMPLATE a gocam:ModelStateEnum ;
rdfs:comment "The model is a template that is not intended to represent a specific biological scenario, but rather to be used as a template for building other models." .
gocam:ModelStateEnum.CLOSED a gocam:ModelStateEnum ;
rdfs:comment "TBD" .
gocam:CellularAnatomicalEntityEnum a rdfs:Class ;
rdfs:comment "A term from the subset of the cellular anatomical entity branch of GO CC" .
gocam:InformationBiomacromoleculeCategory a rdfs:Class ;
rdfs:comment "A term describing the type of the enabler of an activity." .
gocam:biolink.GeneOrGeneProduct a gocam:InformationBiomacromoleculeCategory .
gocam:InformationBiomacromoleculeCategory.PROTEIN_ISOFORM a gocam:InformationBiomacromoleculeCategory .
gocam:InformationBiomacromoleculeCategory.MACROMOLECULAR_COMPLEX a gocam:InformationBiomacromoleculeCategory .
gocam:InformationBiomacromoleculeCategory.UNKNOWN a gocam:InformationBiomacromoleculeCategory .
gocam:EvidenceCodeEnum a rdfs:Class ;
rdfs:comment "A term from the subset of ECO that maps up to a GAF evidence code" .
gocam:CausalPredicateEnum a rdfs:Class ;
rdfs:comment "A term describing the causal relationship between two activities. All terms are drawn from the \"causally upstream or within\" (RO:0002418) branch of the Relation Ontology (RO)." .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .
a gocam:CausalPredicateEnum .