From 76be344faa95ba5332ad983b0ce3b2bc170ddfe1 Mon Sep 17 00:00:00 2001 From: RamonaWalls Date: Sun, 2 May 2021 23:13:58 -0700 Subject: [PATCH] create new release --- imports/bfo_import.obo | 5 +- imports/bfo_import.owl | 6 +- imports/ecocore_import.obo | 5 +- imports/ecocore_import.owl | 31 +- imports/envo_import.obo | 18 +- imports/envo_import.owl | 23 +- imports/go_import.obo | 17 +- imports/go_import.owl | 36 +- imports/iao_import.obo | 3 +- imports/iao_import.owl | 9 +- imports/ncbitaxon_import.obo | 5 +- imports/ncbitaxon_import.owl | 6 +- imports/pato_import.obo | 1372 ++++++++++++++++- imports/pato_import.owl | 981 +----------- imports/ro_import.obo | 3 +- imports/ro_import.owl | 4 +- imports/stato_import.obo | 3 +- imports/stato_import.owl | 63 +- pco-base.obo | 115 +- pco-base.owl | 209 ++- pco-full.obo | 401 ++--- pco-full.owl | 1293 ++++------------ pco.obo | 403 ++--- pco.owl | 1293 ++++------------ reports/pco-edit.owl-obo-report.tsv | 33 +- src/ontology/Makefile | 2 +- src/ontology/catalog-v001.xml | 31 +- src/ontology/imports/pato_import.obo | 2 +- src/ontology/imports/pato_import.owl | 993 +----------- src/ontology/pco-base.obo | 115 +- src/ontology/pco-base.owl | 209 ++- src/ontology/pco-edit.owl | 4 +- src/ontology/pco-full.obo | 401 ++--- src/ontology/pco-full.owl | 1293 ++++------------ src/ontology/pco.obo | 403 ++--- src/ontology/pco.owl | 1293 ++++------------ src/ontology/reports/nolabels-violation.csv | 2 + .../reports/pco-edit.owl-obo-report.tsv | 33 +- 38 files changed, 4266 insertions(+), 6852 deletions(-) create mode 100644 src/ontology/reports/nolabels-violation.csv diff --git a/imports/bfo_import.obo b/imports/bfo_import.obo index c13d079..cd15211 100644 --- a/imports/bfo_import.obo +++ b/imports/bfo_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/bfo_import.obo -ontology: pco/imports/bfo_import.obo +ontology: pco/imports/bfo_import [Term] id: BFO:0000001 @@ -12,7 +11,7 @@ property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string -property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf", comment="per discussion with Barry Smith"} +property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl diff --git a/imports/bfo_import.owl b/imports/bfo_import.owl index aabae7a..48ff81d 100644 --- a/imports/bfo_import.owl +++ b/imports/bfo_import.owl @@ -7,9 +7,7 @@ xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> - - - + @@ -778,5 +776,5 @@ - + diff --git a/imports/ecocore_import.obo b/imports/ecocore_import.obo index 63b4899..37cd64b 100644 --- a/imports/ecocore_import.obo +++ b/imports/ecocore_import.obo @@ -1,6 +1,6 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/ecocore_import.obo -ontology: pco/imports/ecocore_import.obo +data-version: ecocore/releases/2021-02-17/ecocore.owl +ontology: pco/imports/ecocore_import [Term] id: ECOCORE:00000045 @@ -26,6 +26,7 @@ property_value: IAO:0000111 "editor note" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string +property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true diff --git a/imports/ecocore_import.owl b/imports/ecocore_import.owl index 9f4601a..00274ab 100644 --- a/imports/ecocore_import.owl +++ b/imports/ecocore_import.owl @@ -9,7 +9,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + @@ -55,6 +55,7 @@ PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 + has curation status has curation status @@ -64,9 +65,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -93,9 +94,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -108,6 +109,7 @@ We also have the outstanding issue of how to aim different definitions to differ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note @@ -141,9 +143,11 @@ We also have the outstanding issue of how to aim different definitions to differ definition source + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -163,18 +167,13 @@ We also have the outstanding issue of how to aim different definitions to differ - - - has_obo_namespace - + - - - + @@ -186,9 +185,7 @@ We also have the outstanding issue of how to aim different definitions to differ - - shorthand - + @@ -242,5 +239,5 @@ We also have the outstanding issue of how to aim different definitions to differ - + diff --git a/imports/envo_import.obo b/imports/envo_import.obo index 55e2eb5..eb39e29 100644 --- a/imports/envo_import.obo +++ b/imports/envo_import.obo @@ -1,6 +1,22 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/envo_import.owl +data-version: envo/releases/2020-06-10/envo.owl +default-namespace: ENVO +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 499 Logical Axioms: 88] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 114 Logical Axioms: 19] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 135 Logical Axioms: 22] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 40 Logical Axioms: 6] +remark: Includes Ontology(OntologyID(OntologyIRI() VersionIRI())) [Axioms: 21 Logical Axioms: 2] ontology: pco/imports/envo_import +property_value: bug-database https://github.com/EnvironmentOntology/envo/issues/ xsd:anyURI +property_value: GitRepository https://github.com/EnvironmentOntology/envo/ xsd:anyURI +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-4366-3088 +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-6601-2165 xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0002-8343-612X xsd:string +property_value: http://purl.org/dc/elements/1.1/creator http://orcid.org/0000-0003-1604-1512 xsd:string +property_value: http://purl.org/dc/elements/1.1/description "ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities" xsd:string +property_value: http://purl.org/dc/elements/1.1/title "The Environment Ontology" xsd:string +property_value: http://xmlns.com/foaf/0.1/homepage http://environmentontology.org/ xsd:anyURI +property_value: owl:versionInfo "2020-06-10" xsd:string [Term] id: BFO:0000040 diff --git a/imports/envo_import.owl b/imports/envo_import.owl index fda39c8..26bd646 100644 --- a/imports/envo_import.owl +++ b/imports/envo_import.owl @@ -12,8 +12,25 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - + + + + http://orcid.org/0000-0002-6601-2165 + http://orcid.org/0000-0002-8343-612X + http://orcid.org/0000-0003-1604-1512 + ENVO is an ontology which represents knowledge about environments,environmental processes, ecosystems, habitats, and related entities + The Environment Ontology + https://creativecommons.org/publicdomain/zero/1.0/ + https://github.com/EnvironmentOntology/envo/ + https://github.com/EnvironmentOntology/envo/issues/ + ENVO + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 499 Logical Axioms: 88] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 114 Logical Axioms: 19] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>) VersionIRI(<null>))) [Axioms: 135 Logical Axioms: 22] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>) VersionIRI(<null>))) [Axioms: 40 Logical Axioms: 6] + Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>) VersionIRI(<null>))) [Axioms: 21 Logical Axioms: 2] + 2020-06-10 + http://environmentontology.org/ @@ -190,5 +207,5 @@ - + diff --git a/imports/go_import.obo b/imports/go_import.obo index dbf879d..ca7db92 100644 --- a/imports/go_import.obo +++ b/imports/go_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/go_import.obo -ontology: pco/imports/go_import.obo +ontology: pco/imports/go_import [Term] id: GO:0007610 @@ -61,31 +60,37 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0007610 ! behavior -is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 -name: interspecies interaction between organisms +name: biological process involved in interspecies interaction between organisms namespace: biological_process -def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] +subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 -name: intraspecies interaction between organisms +name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] diff --git a/imports/go_import.owl b/imports/go_import.owl index a1444ff..055d35b 100644 --- a/imports/go_import.owl +++ b/imports/go_import.owl @@ -8,9 +8,7 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - + @@ -33,6 +31,14 @@ + + + + + + + + @@ -140,6 +146,14 @@ + + + + + + + + @@ -264,22 +278,25 @@ - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction + interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 + - interspecies interaction between organisms + biological process involved in interspecies interaction between organisms - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. GOC:cc @@ -290,12 +307,15 @@ Any process in which an organism has an effect on an organism of the same species. + https://github.com/geneontology/go-ontology/issues/20191 + intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 + - intraspecies interaction between organisms + biological process involved in intraspecies interaction between organisms @@ -332,5 +352,5 @@ - + diff --git a/imports/iao_import.obo b/imports/iao_import.obo index 2c544ea..d60f8be 100644 --- a/imports/iao_import.obo +++ b/imports/iao_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/iao_import.obo -ontology: pco/imports/iao_import.obo +ontology: pco/imports/iao_import [Typedef] id: IAO:0000136 diff --git a/imports/iao_import.owl b/imports/iao_import.owl index 949800b..c63a130 100644 --- a/imports/iao_import.owl +++ b/imports/iao_import.owl @@ -1,18 +1,13 @@ - - - + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"> + diff --git a/imports/ncbitaxon_import.obo b/imports/ncbitaxon_import.obo index cf87fb0..3a99382 100644 --- a/imports/ncbitaxon_import.obo +++ b/imports/ncbitaxon_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/ncbitaxon_import.obo -ontology: pco/imports/ncbitaxon_import.obo +ontology: pco/imports/ncbitaxon_import [Term] id: NCBITaxon:10239 @@ -384,8 +383,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:4751 name: Fungi namespace: ncbi_taxonomy -synonym: "fungi" RELATED in_part [] synonym: "fungi" RELATED blast_name [] +synonym: "fungi" RELATED in_part [] synonym: "Mycota" RELATED genbank_synonym [] xref: GC_ID:1 xref: PMID:11062127 diff --git a/imports/ncbitaxon_import.owl b/imports/ncbitaxon_import.owl index 33371dd..070368a 100644 --- a/imports/ncbitaxon_import.owl +++ b/imports/ncbitaxon_import.owl @@ -8,9 +8,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - - + @@ -1433,5 +1431,5 @@ - + diff --git a/imports/pato_import.obo b/imports/pato_import.obo index c0ad17f..637a537 100644 --- a/imports/pato_import.obo +++ b/imports/pato_import.obo @@ -1,6 +1,107 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/pato_import.obo ontology: pco/imports/pato_import.obo +owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) + +[Term] +id: BFO:0000002 +name: continuant +def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] +disjoint_from: BFO:0000003 ! occurrent +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000003 +name: occurrent +def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000004 +name: independent continuant +def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000015 +name: process +def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] +is_a: BFO:0000003 ! occurrent +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] +is_a: BFO:0000002 ! continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: BFO:0000040 +name: material entity +def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] +is_a: BFO:0000004 ! independent continuant +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Term] +id: GO:0003674 +name: molecular_function +is_a: BFO:0000015 ! process +property_value: IAO:0000589 "molecular process" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0003824 +name: catalytic activity +is_a: GO:0003674 ! molecular_function +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0008150 +name: biological_process +namespace: biological_process +alt_id: GO:0000004 +alt_id: GO:0007582 +alt_id: GO:0044699 +def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt] +comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. +subset: goslim_aspergillus +subset: goslim_candida +subset: goslim_chembl +subset: goslim_generic +subset: goslim_metagenomics +subset: goslim_pir +subset: goslim_plant +subset: goslim_pombe +subset: goslim_yeast +synonym: "biological process" EXACT [] +synonym: "physiological process" EXACT [] +synonym: "single organism process" RELATED [] +synonym: "single-organism process" RELATED [] +xref: Wikipedia:Biological_process +is_a: BFO:0000015 ! process +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl +created_by: jl +creation_date: 2012-09-19T15:05:24Z + +[Term] +id: GO:0016301 +name: kinase activity +is_a: GO:0016772 ! transferase activity, transferring phosphorus-containing groups +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016740 +name: transferase activity +is_a: GO:0003824 ! catalytic activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl + +[Term] +id: GO:0016772 +name: transferase activity, transferring phosphorus-containing groups +is_a: GO:0016740 ! transferase activity +property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: PATO:0000001 @@ -8,7 +109,45 @@ name: quality namespace: quality alt_id: PATO:0000072 def: "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" [PATOC:GVG] -synonym: "trait" EXACT [] +is_a: BFO:0000020 ! specifically dependent continuant +property_value: IAO:0000589 "quality (PATO)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000068 +name: qualitative +namespace: quality +comment: TODO: define this or obsolete it and move children somewhere else. +is_a: PATO:0000001 ! quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000069 +name: deviation (from_normal) +namespace: quality +def: "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." [PATOC:GVG] +subset: attribute_slim +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0000070 +name: amount +namespace: quality +alt_id: PATO:0000053 +alt_id: PATO:0000071 +alt_id: PATO:0001169 +alt_id: PATO:0001226 +def: "The number of entities of this type that are part of the whole organism." [PATOC:GVG] +comment: This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. +subset: attribute_slim +synonym: "count in organism" RELATED [] +synonym: "number" RELATED [] +synonym: "presence" RELATED [] +synonym: "presence or absence in organism" EXACT [] +synonym: "quantitative" EXACT [] +is_a: PATO:0000068 ! qualitative +relationship: reciprocal_of PATO:0001555 ! has number of property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -21,6 +160,115 @@ subset: scalar_slim is_a: PATO:0002062 ! physical quality of a process property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0000461 +name: normal +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." [PATOC:GVG] +subset: abnormal_slim +subset: mpath_slim +subset: value_slim +synonym: "average" RELATED [] +is_a: PATO:0000068 ! qualitative +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000460 + +[Term] +id: PATO:0000467 +name: present +namespace: quality +def: "A quality inhering in a bearer by virtue of the bearer's existence." [PATOC:GVG] +subset: absent_slim +subset: value_slim +synonym: "present in organism" RELATED [] +is_a: PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000462 + +[Term] +id: PATO:0000470 +name: increased amount +namespace: quality +alt_id: PATO:0000420 +alt_id: PATO:0000650 +def: "An amount which is relatively high." [PATOC:GVG] +subset: value_slim +synonym: "accessory" RELATED [] +synonym: "increased" RELATED [] +synonym: "increased number" EXACT [] +synonym: "present in greater numbers in organism" EXACT [] +synonym: "supernumerary" EXACT [] +is_a: PATO:0000467 ! present +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0000070 ! amount +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001997 + +[Term] +id: PATO:0000911 +name: decreased rate +namespace: quality +def: "A rate which is relatively low." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "slow rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002302 ! decreased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000912 + +[Term] +id: PATO:0000912 +name: increased rate +namespace: quality +def: "A rate which is relatively high." [PATO:GVG] +subset: mpath_slim +subset: value_slim +synonym: "fast rate" EXACT [] +synonym: "high rate" EXACT [] +is_a: PATO:0000161 ! rate +is_a: PATO:0002304 ! increased process quality +intersection_of: PATO:0000161 ! rate +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000911 + +[Term] +id: PATO:0001018 +name: physical quality +namespace: quality +alt_id: PATO:0002079 +def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [PATOC:GVG] +subset: attribute_slim +synonym: "relational physical quality" EXACT [] +xref: Wikipedia:Physical_property +is_a: PATO:0001241 ! physical object quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001019 +name: mass density +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size." [WordNet:WordNet] +subset: attribute_slim +subset: scalar_slim +synonym: "density" RELATED [] +is_a: PATO:0001018 ! physical quality +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001164 +name: dense +namespace: quality +def: "A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density." [PATOC:GVG] +subset: mpath_slim +subset: value_slim +is_a: PATO:0001019 ! mass density +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + [Term] id: PATO:0001236 name: process quality @@ -34,6 +282,7 @@ synonym: "quality of occurrent" EXACT [] synonym: "quality of process" EXACT [] synonym: "relational quality of occurrent" EXACT [] is_a: PATO:0000001 ! quality +disjoint_from: PATO:0001241 ! physical object quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl [Term] @@ -76,6 +325,72 @@ subset: scalar_slim is_a: PATO:0002003 ! population quality property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +[Term] +id: PATO:0001555 +name: has number of +namespace: quality +def: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts." [PATOC:CJM] +subset: attribute_slim +subset: relational_slim +synonym: "cardinality" RELATED [] +synonym: "extra or missing physical or functional parts" EXACT [] +synonym: "has or lacks parts of type" EXACT [] +synonym: "mereological quality" EXACT [] +synonym: "number" RELATED [] +synonym: "number of" EXACT [] +xref: OBO_REL:has_part +is_a: PATO:0001241 ! physical object quality +relationship: reciprocal_of PATO:0000070 ! amount +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + +[Term] +id: PATO:0001788 +name: increased mass density +namespace: quality +def: "A density which is higher relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "high density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002305 ! increased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001790 + +[Term] +id: PATO:0001790 +name: decreased mass density +namespace: quality +def: "A density which is lower relative to the normal or average." [PATOC:GVG] +subset: value_slim +synonym: "low density" EXACT [] +is_a: PATO:0001164 ! dense +is_a: PATO:0002303 ! decreased object quality +intersection_of: PATO:0001164 ! dense +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0001788 + +[Term] +id: PATO:0001997 +name: decreased amount +namespace: quality +alt_id: PATO:0000419 +alt_id: PATO:0000468 +def: "An amount which is relatively low." [PATOC:GVG] +subset: value_slim +synonym: "decreased" RELATED [] +synonym: "decreased number" EXACT [] +synonym: "present in fewer numbers in organism" EXACT [] +synonym: "reduced" RELATED [] +synonym: "subnumerary" RELATED [] +is_a: PATO:0000467 ! present +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0000070 ! amount +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0000470 + [Term] id: PATO:0002003 name: population quality @@ -95,3 +410,1056 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl created_by: george creation_date: 2009-06-05T09:16:46Z +[Term] +id: PATO:0002300 +name: increased quality +namespace: quality +def: "A quality that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002301 +created_by: George Gkoutos +creation_date: 2011-06-16T06:39:43Z + +[Term] +id: PATO:0002301 +name: decreased quality +namespace: quality +def: "A quality that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0000069 ! deviation (from_normal) +intersection_of: PATO:0000001 ! quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +relationship: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002300 +created_by: George Gkoutos +creation_date: 2011-06-16T06:40:15Z + +[Term] +id: PATO:0002302 +name: decreased process quality +namespace: quality +def: "A quality of a process that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002304 +created_by: George Gkoutos +creation_date: 2011-06-16T06:50:59Z + +[Term] +id: PATO:0002303 +name: decreased object quality +namespace: quality +def: "A quality of an object that has a value that is decreased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002301 ! decreased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: decreased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002305 +created_by: George Gkoutos +creation_date: 2011-06-16T06:51:54Z + +[Term] +id: PATO:0002304 +name: increased process quality +namespace: quality +def: "A quality of a process that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001236 ! process quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001236 ! process quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002302 +created_by: George Gkoutos +creation_date: 2011-06-16T06:53:08Z + +[Term] +id: PATO:0002305 +name: increased object quality +namespace: quality +def: "A quality of an object that has a value that is increased compared to normal or average." [PATOC:GVG] +is_a: PATO:0001241 ! physical object quality +is_a: PATO:0002300 ! increased quality +intersection_of: PATO:0001241 ! physical object quality +intersection_of: increased_in_magnitude_relative_to PATO:0000461 ! normal +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +property_value: RO:0002604 PATO:0002303 +created_by: George Gkoutos +creation_date: 2011-06-16T06:54:01Z + +[Typedef] +id: BFO:0000062 +name: preceded by +def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string +property_value: IAO:0000111 "preceded by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string +property_value: IAO:0000118 "is preceded by" xsd:string +property_value: IAO:0000118 "preceded_by" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_transitive: true +is_a: RO:0002086 ! ends after +inverse_of: BFO:0000063 ! precedes + +[Typedef] +id: BFO:0000063 +name: precedes +def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] +subset: ro-eco +property_value: IAO:0000111 "precedes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: BFO:0000066 +name: occurs in +def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000111 "occurs in" xsd:string +property_value: IAO:0000118 "occurs_in" xsd:string +property_value: IAO:0000118 "unfolds in" xsd:string +property_value: IAO:0000118 "unfolds_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant +inverse_of: BFO:0000067 ! contains process + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant +property_value: IAO:0000111 "site of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl + +[Typedef] +id: RO:0000056 +name: participates in +def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] +property_value: IAO:0000111 "participates in" xsd:string +property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string +property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string +property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string +property_value: IAO:0000118 "participates_in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000003 ! occurrent +inverse_of: RO:0000057 ! has participant + +[Typedef] +id: RO:0000057 +name: has participant +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string +property_value: IAO:0000111 "has participant" xsd:string +property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string +property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string +property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +property_value: IAO:0000118 "has_participant" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant + +[Typedef] +id: RO:0002022 +name: directly regulated by +comment: Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. {xref="GOC:dos"} +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by +inverse_of: RO:0002578 ! directly regulates +created_by: dos +creation_date: 2017-09-17T13:52:24Z + +[Typedef] +id: RO:0002023 +name: directly negatively regulated by +def: "Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002630 ! directly negatively regulates +created_by: dos +creation_date: 2017-09-17T13:52:38Z + +[Typedef] +id: RO:0002024 +name: directly positively regulated by +def: "Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1." [GOC:dos] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002022 ! directly regulated by +inverse_of: RO:0002629 ! directly positively regulates +created_by: dos +creation_date: 2017-09-17T13:52:47Z + +[Typedef] +id: RO:0002086 +name: ends after +comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002222 ! temporally related to + +[Typedef] +id: RO:0002087 +name: immediately preceded by +comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "starts_at_end_of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +inverse_of: RO:0002090 ! immediately precedes + +[Typedef] +id: RO:0002090 +name: immediately precedes +comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) +subset: ro-eco +property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string +property_value: IAO:0000118 "ends_at_start_of" xsd:string +property_value: IAO:0000118 "meets" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 BFO:0000063 +is_a: BFO:0000063 ! precedes + +[Typedef] +id: RO:0002131 +name: overlaps +def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 +is_a: RO:0002323 ! mereotopologically related to +expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] + +[Typedef] +id: RO:0002211 +name: regulates +def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000116 "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "David Hill" xsd:string +property_value: IAO:0000117 "Tanya Berardini" xsd:string +property_value: IAO:0000119 "GO" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string +property_value: IAO:0000589 "regulates (processual)" xsd:string +property_value: IAO:0000600 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +holds_over_chain: RO:0002578 RO:0002578 +is_transitive: true +is_a: RO:0002411 ! causally upstream of +inverse_of: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002212 +name: negatively regulates +def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002305 ! causally upstream of, negative effect +inverse_of: RO:0002335 ! negatively regulated by + +[Typedef] +id: RO:0002213 +name: positively regulates +def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002211 +holds_over_chain: RO:0002212 RO:0002212 +is_transitive: true +is_a: RO:0002211 ! regulates +is_a: RO:0002304 ! causally upstream of, positive effect +inverse_of: RO:0002336 ! positively regulated by + +[Typedef] +id: RO:0002215 +name: capable of +def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] +subset: ro-eco +property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string +property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function realized in" xsd:string +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 +property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 +property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000004 ! independent continuant +range: BFO:0000015 ! process +is_a: RO:0002216 ! capable of part of + +[Typedef] +id: RO:0002216 +name: capable of part of +def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "has function in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso "defining-property-chains-involving-reflexivity" +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002222 +name: temporally related to +comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. +subset: ro-eco +property_value: http://purl.org/dc/terms/source https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 xsd:anyURI +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent + +[Typedef] +id: RO:0002233 +name: has input +def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +subset: ro-eco +property_value: IAO:0000114 IAO:0000125 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "consumes" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +is_a: RO:0000057 ! has participant +inverse_of: RO:0002352 ! input of + +[Typedef] +id: RO:0002263 +name: acts upstream of +def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of +holds_over_chain: RO:0002327 RO:0002411 +is_a: RO:0002264 ! acts upstream of or within + +[Typedef] +id: RO:0002264 +name: acts upstream of or within +def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +synonym: "affects" RELATED [] +property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within +holds_over_chain: RO:0002327 RO:0002418 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002304 +name: causally upstream of, positive effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004047 ! causally upstream of or within, positive effect + +[Typedef] +id: RO:0002305 +name: causally upstream of, negative effect +comment: holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y +property_value: http://purl.org/dc/terms/creator "cjm" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002411 +is_a: RO:0002411 ! causally upstream of +is_a: RO:0004046 ! causally upstream of or within, negative effect + +[Typedef] +id: RO:0002323 +name: mereotopologically related to +def: "A mereological relationship or a topological relationship" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0001900 RO:0001901 + +[Typedef] +id: RO:0002327 +name: enables +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "catalyzes" xsd:string +property_value: IAO:0000118 "executes" xsd:string +property_value: IAO:0000118 "has" xsd:string +property_value: IAO:0000118 "is catalyzing" xsd:string +property_value: IAO:0000118 "is executing" xsd:string +property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string +property_value: IAO:0000232 "This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002215 ! capable of +inverse_of: RO:0002333 ! enabled by + +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002329 +name: part of structure that is capable of +def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "false" xsd:boolean +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002331 +name: involved in +def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "actively involved in" xsd:string +property_value: IAO:0000118 "enables part of" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso Involved:in +is_a: RO:0000056 ! participates in +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002333 +name: enabled by +def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000057 ! has participant +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002334 +name: regulated by +def: "inverse of regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000589 "regulated by (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000015 ! process +range: BFO:0000015 ! process +is_transitive: true +is_a: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002335 +name: negatively regulated by +def: "inverse of negatively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002336 +name: positively regulated by +def: "inverse of positively regulates" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002334 ! regulated by + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0000056 ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002404 +name: causally downstream of +def: "inverse of upstream of" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: BFO:0000062 ! preceded by +is_a: RO:0002427 ! causally downstream of or within +inverse_of: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002405 +name: immediately causally downstream of +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002087 ! immediately preceded by +is_a: RO:0002404 ! causally downstream of +inverse_of: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002410 +name: causally related to +def: "This relation groups causal relations between material entities and causal relations between processes" [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002411 +name: causally upstream of +def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: BFO:0000063 ! precedes +is_a: RO:0002418 ! causally upstream of or within + +[Typedef] +id: RO:0002412 +name: immediately causally upstream of +def: "p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q." [] +property_value: IAO:0000114 IAO:0000428 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002411 +is_a: RO:0002090 ! immediately precedes +is_a: RO:0002411 ! causally upstream of + +[Typedef] +id: RO:0002418 +name: causally upstream of or within +def: "p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q." [] +synonym: "affects" RELATED [] +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes +inverse_of: RO:0002427 ! causally downstream of or within + +[Typedef] +id: RO:0002427 +name: causally downstream of or within +def: "inverse of causally upstream of or within" [] +subset: RO:0002259 +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_transitive: true +is_a: RO:0002501 ! causal relation between processes + +[Typedef] +id: RO:0002428 +name: involved in regulation of +def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 RO:0002211 +holds_over_chain: RO:0002331 RO:0002211 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0002431 ! involved in or involved in regulation of + +[Typedef] +id: RO:0002429 +name: involved in positive regulation of +def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002428 +holds_over_chain: RO:0002327 RO:0002213 +holds_over_chain: RO:0002331 RO:0002213 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002430 +name: involved in negative regulation of +def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002428 +holds_over_chain: RO:0002327 RO:0002212 +holds_over_chain: RO:0002331 RO:0002212 +is_a: RO:0002428 ! involved in regulation of + +[Typedef] +id: RO:0002431 +name: involved in or involved in regulation of +def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "involved in or reguates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002432 +name: is active in +def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [GOC:cjm, GOC:dos] +synonym: "enables activity in" EXACT [] +property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "executes activity in" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002327 BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} +is_a: RO:0002131 ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002434 +name: interacts with +def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] +subset: ro-eco +synonym: "in pairwise interaction with" EXACT [] +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0914 xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_symmetric: true + +[Typedef] +id: RO:0002436 +name: molecularly interacts with +def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "binds" xsd:string +property_value: IAO:0000118 "molecularly binds with" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso ECO:0000353 +property_value: seeAlso http://purl.obolibrary.org/obo/MI_0915 xsd:anyURI +is_symmetric: true +is_a: RO:0002434 ! interacts with + +[Typedef] +id: RO:0002447 +name: phosphorylates +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002436 ! molecularly interacts with + +[Typedef] +id: RO:0002448 +name: directly regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] +synonym: "molecularly controls" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002436 ! molecularly interacts with +is_a: RO:0011002 ! regulates activity of + +[Typedef] +id: RO:0002449 +name: directly negatively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] +synonym: "molecularly decreases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly inhibits" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002450 +name: directly positively regulates activity of +def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] +synonym: "molecularly increases activity of" EXACT [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000118 "directly activates" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002448 ! directly regulates activity of + +[Typedef] +id: RO:0002464 +name: helper property (not for use in curation) +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl + +[Typedef] +id: RO:0002479 +name: has part that occurs in +def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] +subset: ro-eco +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000004 ! independent continuant + +[Typedef] +id: RO:0002481 +name: is kinase activity +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002564 ! molecular interaction relation helper property + +[Typedef] +id: RO:0002500 +name: causal agent in process +def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002595 ! causal relation between material entity and a process +inverse_of: RO:0002608 ! process has causal agent + +[Typedef] +id: RO:0002501 +name: causal relation between processes +def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000003 ! occurrent +range: BFO:0000003 ! occurrent +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002506 +name: causal relation between entities +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002559 +name: causally influenced by +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002506 ! causal relation between entities +inverse_of: RO:0002566 ! causally influences + +[Typedef] +id: RO:0002563 +name: interaction relation helper property +property_value: http://xmlns.com/foaf/0.1/page https://github.com/oborel/obo-relations/wiki/InteractionRelations xsd:anyURI +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 +is_a: RO:0002464 ! helper property (not for use in curation) + +[Typedef] +id: RO:0002564 +name: molecular interaction relation helper property +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002563 ! interaction relation helper property + +[Typedef] +id: RO:0002566 +name: causally influences +def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +is_a: RO:0002506 ! causal relation between entities + +[Typedef] +id: RO:0002578 +name: directly regulates +def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly regulates (processual)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0002575 RO:0002211 +is_a: RO:0002211 ! regulates +is_a: RO:0002412 ! immediately causally upstream of + +[Typedef] +id: RO:0002584 +name: has part structure that is capable of +def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] +property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002328 ! functionally related to +is_a: RO:0002595 ! causal relation between material entity and a process + +[Typedef] +id: RO:0002595 +name: causal relation between material entity and a process +def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000117 "Chris Mungall" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000015 ! process +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002596 +name: capable of regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] +property_value: IAO:0000112 "pyrethroid -> growth" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002211 +is_a: RO:0002500 ! causal agent in process + +[Typedef] +id: RO:0002597 +name: capable of negatively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002212 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002598 +name: capable of positively regulating +def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] +property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +holds_over_chain: RO:0002215 RO:0002213 +is_a: RO:0002596 ! capable of regulating + +[Typedef] +id: RO:0002608 +name: process has causal agent +def: "Inverse of 'causal agent in process'" [] +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002410 ! causally related to + +[Typedef] +id: RO:0002629 +name: directly positively regulates +def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002578 +is_a: RO:0002213 ! positively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0002630 +name: directly negatively regulates +def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002578 +is_a: RO:0002212 ! negatively regulates +is_a: RO:0002578 ! directly regulates + +[Typedef] +id: RO:0004031 +name: enables subfunction +def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +is_a: RO:0002328 ! functionally related to +created_by: cjm +creation_date: 2018-01-25T23:20:13Z + +[Typedef] +id: RO:0004032 +name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002264 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect +holds_over_chain: RO:0002327 RO:0004047 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:30Z + +[Typedef] +id: RO:0004033 +name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002264 +holds_over_chain: RO:0002327 RO:0004046 +is_a: RO:0002264 ! acts upstream of or within +created_by: cjm +creation_date: 2018-01-26T23:49:51Z + +[Typedef] +id: RO:0004034 +name: acts upstream of, positive effect +def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect +holds_over_chain: RO:0002327 RO:0002304 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004032 ! acts upstream of or within, positive effect +created_by: cjm +creation_date: 2018-01-26T23:53:14Z + +[Typedef] +id: RO:0004035 +name: acts upstream of, negative effect +def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002263 +property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect +holds_over_chain: RO:0002327 RO:0002305 +is_a: RO:0002263 ! acts upstream of +is_a: RO:0004033 ! acts upstream of or within, negative effect +created_by: cjm +creation_date: 2018-01-26T23:53:22Z + +[Typedef] +id: RO:0004046 +name: causally upstream of or within, negative effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004050 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:05Z + +[Typedef] +id: RO:0004047 +name: causally upstream of or within, positive effect +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +property_value: RO:0004049 RO:0002418 +is_a: RO:0002418 ! causally upstream of or within +created_by: cjm +creation_date: 2018-03-13T23:55:19Z + +[Typedef] +id: RO:0011002 +name: regulates activity of +def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] +property_value: IAO:0000117 "Vasundra Touré" xsd:string +property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002566 ! causally influences + +[Typedef] +id: decreased_in_magnitude_relative_to +name: decreased_in_magnitude_relative_to +namespace: quality +def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: different_in_magnitude_relative_to +name: different_in_magnitude_relative_to +namespace: quality +def: "q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality + +[Typedef] +id: increased_in_magnitude_relative_to +name: increased_in_magnitude_relative_to +namespace: quality +def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM] +comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl +domain: PATO:0000001 ! quality +range: PATO:0000001 ! quality +is_transitive: true +is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to + +[Typedef] +id: reciprocal_of +name: reciprocal_of +namespace: quality +def: "q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e." [PATOC:CJM] +comment: There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. +property_value: isDefinedBy http://purl.obolibrary.org/obo/pato.owl + diff --git a/imports/pato_import.owl b/imports/pato_import.owl index 510070d..eaa5967 100644 --- a/imports/pato_import.owl +++ b/imports/pato_import.owl @@ -14,9 +14,7 @@ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - + @@ -417,85 +415,6 @@ - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - - BFO:0000050 - external - quality - part_of - part_of - - part of - part of - part_of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - BFO:0000051 - external - quality - has_part - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part - has part - has_part - - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - - - - @@ -504,10 +423,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -528,10 +443,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -547,19 +458,14 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in @@ -602,10 +508,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -620,78 +522,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -752,28 +582,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -822,56 +630,16 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -898,6 +666,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false + + + regulates @@ -915,6 +686,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. negatively regulates (process to process) + + + negatively regulates @@ -937,6 +711,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. positively regulates (process to process) + + + positively regulates @@ -957,7 +734,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) capable of @@ -970,27 +746,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of - - - - - - - - true - @@ -1018,11 +780,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes + + + has input @@ -1040,6 +804,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -1058,6 +823,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects + acts upstream of or within @@ -1072,6 +838,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. cjm + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -1111,14 +879,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -1128,6 +888,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables @@ -1150,25 +911,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -1177,14 +925,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -1203,6 +943,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. inverse of enables Chris Mungall + enabled by @@ -1333,6 +1074,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall + + causally upstream of @@ -1496,7 +1239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm + GOC:cjm GOC:dos @@ -1639,25 +1382,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -1792,6 +1522,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly regulates (processual) + + + directly regulates @@ -1803,10 +1536,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -1903,6 +1632,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates (process to process) + + + directly positively regulates @@ -1918,6 +1650,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates (process to process) + + + directly negatively regulates @@ -1928,10 +1663,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -1952,6 +1683,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:30Z + acts upstream of or within, positive effect @@ -1970,6 +1702,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:51Z + acts upstream of or within, negative effect @@ -1989,6 +1722,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -2009,6 +1743,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -2155,19 +1890,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant @@ -2178,18 +1901,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -2201,12 +1912,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. @@ -2230,12 +1935,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -2309,7 +2008,7 @@ For example, A and B may be gene products and binding of B by A positively regul A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. - GOC:pdt + GOC:pdt @@ -3176,6 +2875,14 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + - - - - - - @@ -3243,15 +2944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - @@ -3264,85 +2956,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -3414,124 +3036,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -3602,7 +3106,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -3610,7 +3114,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -3621,274 +3125,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - + + + @@ -3901,28 +3140,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - + + + @@ -3930,34 +3150,19 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -3965,9 +3170,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -3976,9 +3181,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -3991,28 +3196,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - + + + @@ -4020,30 +3206,15 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - diff --git a/imports/ro_import.obo b/imports/ro_import.obo index aa9b7f2..685b747 100644 --- a/imports/ro_import.obo +++ b/imports/ro_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/ro_import.obo -ontology: pco/imports/ro_import.obo +ontology: pco/imports/ro_import [Typedef] id: RO:0002321 diff --git a/imports/ro_import.owl b/imports/ro_import.owl index c49c1d8..c1d4845 100644 --- a/imports/ro_import.owl +++ b/imports/ro_import.owl @@ -11,9 +11,7 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - - - + diff --git a/imports/stato_import.obo b/imports/stato_import.obo index c6dcab1..faf4fd2 100644 --- a/imports/stato_import.obo +++ b/imports/stato_import.obo @@ -1,6 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/imports/stato_import.obo -ontology: pco/imports/stato_import.obo +ontology: pco/imports/stato_import [Term] id: IAO:0000027 diff --git a/imports/stato_import.owl b/imports/stato_import.owl index 3000f3d..75f3f9d 100644 --- a/imports/stato_import.owl +++ b/imports/stato_import.owl @@ -11,7 +11,6 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/"> - Camille Maumet (http://orcid.org/0000-0002-6290-553X) Chris Mungall (http://orcid.org/0000-0002-6601-2165) Hanna Cwiek (https://orcid.org/0000-0001-9113-567X) @@ -217,66 +216,6 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -367,5 +306,5 @@ JAR: A data item is an approximately justified approximately true approximate be - + diff --git a/pco-base.obo b/pco-base.obo index 89d34f8..19cf037 100644 --- a/pco-base.obo +++ b/pco-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/pco-base.owl +data-version: pco/releases/2021-05-03/pco-base.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-base property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -60,7 +60,7 @@ id: PCO:0000000 name: collection of organisms def: "A material entity that consists of two or more organisms, viruses, or viroids." [] comment: May be of the same or different species. -is_a: BFO:0000027 +intersection_of: BFO:0000027 intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid @@ -221,9 +221,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -617,19 +614,116 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] -is_a: BFO:0000040 -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] +is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -682,6 +776,7 @@ property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true diff --git a/pco-base.owl b/pco-base.owl index d554572..0e81848 100644 --- a/pco-base.owl +++ b/pco-base.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -146,6 +146,12 @@ + + + + + + @@ -184,11 +190,9 @@ - - - - - has member of + + obsolete has member of + true @@ -390,6 +394,12 @@ + + + + + + @@ -414,6 +424,7 @@ + @@ -426,7 +437,6 @@ - @@ -705,26 +715,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. @@ -1326,17 +1316,157 @@ Classes for population already exist in IDO ('organism population', I + + + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria + + + + + + + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity + + + + + + + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity + + + + + + + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + - - - - - 2 - - - + + + + + + + 2 + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms @@ -1346,14 +1476,9 @@ Classes for population already exist in IDO ('organism population', I + - - - - 1 - - - + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species diff --git a/pco-full.obo b/pco-full.obo index 08e5f17..414bee3 100644 --- a/pco-full.obo +++ b/pco-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/pco-full.owl +data-version: pco/releases/2021-05-03/pco-full.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-full property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -32,7 +32,6 @@ name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string @@ -52,7 +51,6 @@ id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity -relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string @@ -74,7 +72,6 @@ def: "b is an independent continuant = Def. b is a continuant which is such that is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -98,7 +95,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl id: BFO:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_obsolete: true [Term] @@ -163,7 +160,6 @@ def: "A continuant that inheres in or is borne by other entities. Every instance def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} @@ -467,31 +463,37 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0007610 ! behavior -is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 -name: interspecies interaction between organisms +name: biological process involved in interspecies interaction between organisms namespace: biological_process -def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] +subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 -name: intraspecies interaction between organisms +name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -1301,10 +1303,6 @@ is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: ObsoleteClass -name: Obsolete Class - [Term] id: PATO:0000001 name: quality @@ -1703,6 +1701,7 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity +intersection_of: BFO:0000027 ! object aggregate intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid @@ -1791,7 +1790,7 @@ property_value: IAO:0000114 IAO:0000123 id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 @@ -1830,21 +1829,21 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 name: obsolete predator role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 name: obsolete prey role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 name: obsolete symbiont role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} @@ -1868,10 +1867,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid -relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1922,7 +1917,7 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000000 ! collection of organisms +is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 @@ -1933,7 +1928,7 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:st id: PCO:0000025 name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1941,7 +1936,7 @@ is_obsolete: true id: PCO:0000026 name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1963,7 +1958,7 @@ id: PCO:0000028 name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1983,7 +1978,7 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_a: PCO:0000024 ! household property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2064,7 +2059,7 @@ def: "An ecological community which is composed primarily of dwarf or short mang synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2074,7 +2069,7 @@ id: PCO:0000041 name: obsolete invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2082,7 +2077,7 @@ is_obsolete: true id: PCO:0000042 name: obsolete microbe synonym: "microbial organism" EXACT [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2090,7 +2085,7 @@ is_obsolete: true id: PCO:0000043 name: obsolete collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2099,7 +2094,7 @@ is_obsolete: true id: PCO:0000044 name: obsolete multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2108,7 +2103,7 @@ is_obsolete: true id: PCO:0000045 name: obsolete single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2118,7 +2113,7 @@ id: PCO:0000046 name: obsolete microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2131,7 +2126,7 @@ synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: part_of ENVO:01001369 ! tidal mangrove shrubland +relationship: BFO:0000050 ENVO:01001369 ! part of tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] @@ -2151,7 +2146,6 @@ is_a: CARO:0001010 ! organism or virus or viroid id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: PCO:0000000 ! collection of organisms intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe relationship: RO:0002351 PCO:0000049 ! has member microbe @@ -2271,12 +2265,109 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 ! mass density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 @@ -2284,7 +2375,7 @@ name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -2348,6 +2439,38 @@ property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "STATO" xsd:string property_value: STATO:0000032 "" xsd:string +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + [Typedef] id: BFO:0000054 name: realized in @@ -2390,7 +2513,6 @@ property_value: IAO:0000118 "preceded_by" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -2404,7 +2526,6 @@ property_value: IAO:0000111 "precedes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2413,6 +2534,9 @@ id: BFO:0000066 name: occurs in def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string @@ -2420,9 +2544,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 +holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 @@ -2444,8 +2568,9 @@ property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosop [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true [Typedef] id: RO:0000052 @@ -2500,7 +2625,6 @@ property_value: IAO:0000118 "has_participant" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000058 @@ -2678,58 +2802,6 @@ property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - [Typedef] id: RO:0002022 name: directly regulated by @@ -2760,18 +2832,6 @@ inverse_of: RO:0002629 ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002086 name: ends after @@ -2808,34 +2868,22 @@ is_a: BFO:0000063 ! precedes id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: has_part RO:0002131 -holds_over_chain: part_of part_of is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: RO:0002211 name: regulates def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2858,6 +2906,9 @@ inverse_of: RO:0002334 ! regulated by id: RO:0002212 name: negatively regulates def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -2871,6 +2922,9 @@ inverse_of: RO:0002335 ! negatively regulated by id: RO:0002213 name: positively regulates def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2898,7 +2952,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] [Typedef] id: RO:0002216 @@ -2908,10 +2961,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002222 @@ -2931,13 +2982,15 @@ range: BFO:0000003 ! occurrent id: RO:0002233 name: has input def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "consumes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -2945,6 +2998,7 @@ inverse_of: RO:0002352 ! input of id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of @@ -2955,6 +3009,7 @@ is_a: RO:0002264 ! acts upstream of or within id: RO:0002264 name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -2966,6 +3021,8 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002411 @@ -3003,6 +3060,7 @@ property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002327 name: enables +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -3015,8 +3073,6 @@ property_value: IAO:0000232 "This relation is currently used experimentally by t property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part -transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3033,7 +3089,6 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "false" xsd:boolean property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3045,15 +3100,14 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 part_of is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0000057 ! has participant @@ -3099,7 +3153,7 @@ property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -3108,7 +3162,7 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -3156,6 +3210,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl id: RO:0002411 name: causally upstream of def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3350,7 +3406,6 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] id: RO:0002481 @@ -3435,6 +3490,9 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002578 name: directly regulates def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3450,7 +3508,6 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: has_part RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3507,6 +3564,9 @@ is_a: RO:0002410 ! causally related to id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3518,6 +3578,9 @@ is_a: RO:0002578 ! directly regulates id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3530,7 +3593,6 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: cjm creation_date: 2018-01-25T23:20:13Z @@ -3538,6 +3600,7 @@ creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect @@ -3549,6 +3612,7 @@ creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 @@ -3560,6 +3624,7 @@ creation_date: 2018-01-26T23:49:51Z id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect @@ -3573,6 +3638,7 @@ creation_date: 2018-01-26T23:53:14Z id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect @@ -3645,29 +3711,6 @@ property_value: IAO:0000119 GROUP:OBI: xsd:s property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true -[Typedef] -id: has_part -name: has part -name: has_part -namespace: external -namespace: quality -def: "a core relation that holds between a whole and its part" [] -def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] -comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. -xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to @@ -3680,38 +3723,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: part_of -name: part of -name: part_of -namespace: external -namespace: quality -def: "a core relation that holds between a part and its whole" [] -xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: has_part ! has part - [Typedef] id: reciprocal_of name: reciprocal_of diff --git a/pco-full.owl b/pco-full.owl index b73706e..a8b8623 100644 --- a/pco-full.owl +++ b/pco-full.owl @@ -17,7 +17,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -132,9 +132,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -161,9 +161,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -227,8 +227,8 @@ We also have the outstanding issue of how to aim different definitions to differ Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -272,6 +272,7 @@ We also have the outstanding issue of how to aim different definitions to differ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item @@ -870,7 +871,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace @@ -919,7 +919,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - shorthand @@ -1031,7 +1030,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - is part of @@ -1046,24 +1044,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - - - - - - - - BFO:0000050 - external - quality - part_of - part_of - - part of part of - part_of - - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1072,13 +1053,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime @@ -1087,23 +1066,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - external - quality - has_part - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part has part - has_part - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - @@ -1152,10 +1116,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -1176,10 +1136,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -1208,6 +1164,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in unfolds in unfolds_in + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in @@ -1248,11 +1207,9 @@ Some currently missing phenomena that should be considered "about" are - - - - - has member of + + obsolete has member of + true @@ -1313,10 +1270,6 @@ Some currently missing phenomena that should be considered "about" are - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -1555,13 +1508,13 @@ Some currently missing phenomena that should be considered "about" are - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. @@ -1603,78 +1556,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -1735,28 +1616,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -1805,56 +1664,16 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -1881,6 +1700,9 @@ Some currently missing phenomena that should be considered "about" are Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false + + + regulates @@ -1898,6 +1720,9 @@ Some currently missing phenomena that should be considered "about" are negatively regulates (process to process) + + + negatively regulates @@ -1920,6 +1745,9 @@ Some currently missing phenomena that should be considered "about" are positively regulates (process to process) + + + positively regulates @@ -1940,7 +1768,6 @@ Some currently missing phenomena that should be considered "about" are For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) capable of @@ -1953,27 +1780,13 @@ Some currently missing phenomena that should be considered "about" are - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of - - - - - - - - true - @@ -2001,11 +1814,13 @@ Some currently missing phenomena that should be considered "about" are - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes + + + has input @@ -2023,6 +1838,7 @@ Some currently missing phenomena that should be considered "about" are A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -2041,6 +1857,7 @@ Some currently missing phenomena that should be considered "about" are A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects + acts upstream of or within @@ -2055,6 +1872,8 @@ Some currently missing phenomena that should be considered "about" are cjm + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2107,14 +1926,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -2124,6 +1935,7 @@ Some currently missing phenomena that should be considered "about" are is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables @@ -2146,25 +1958,12 @@ Some currently missing phenomena that should be considered "about" are - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -2173,14 +1972,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -2199,6 +1990,7 @@ Some currently missing phenomena that should be considered "about" are inverse of enables Chris Mungall + enabled by @@ -2358,6 +2150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall + + causally upstream of @@ -2521,7 +2315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm + GOC:cjm GOC:dos @@ -2664,25 +2458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -2817,6 +2598,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly regulates (processual) + + + directly regulates @@ -2828,10 +2612,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -2928,6 +2708,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates (process to process) + + + directly positively regulates @@ -2943,6 +2726,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates (process to process) + + + directly negatively regulates @@ -2953,10 +2739,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -2977,6 +2759,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:30Z + acts upstream of or within, positive effect @@ -2995,6 +2778,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:51Z + acts upstream of or within, negative effect @@ -3014,6 +2798,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -3034,6 +2819,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -3213,12 +2999,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3303,12 +3083,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3380,12 +3154,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - ic @@ -3410,6 +3178,12 @@ For example, A and B may be gene products and binding of B by A positively regul independent continuant + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + @@ -3440,12 +3214,6 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - @@ -3575,12 +3343,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - sdc SpecificallyDependentContinuant @@ -4145,22 +3907,25 @@ For example, A and B may be gene products and binding of B by A positively regul - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction + interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 + - interspecies interaction between organisms + biological process involved in interspecies interaction between organisms - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. GOC:cc @@ -4171,12 +3936,15 @@ For example, A and B may be gene products and binding of B by A positively regul Any process in which an organism has an effect on an organism of the same species. + https://github.com/geneontology/go-ontology/issues/20191 + intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 + - intraspecies interaction between organisms + biological process involved in intraspecies interaction between organisms @@ -6772,6 +6540,7 @@ No imports + @@ -7084,33 +6853,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -7185,7 +6928,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -7489,7 +7232,6 @@ Classes for population already exist in IDO ('organism population', I - @@ -7732,61 +7474,196 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - 2 - - - - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria - + - - - - - - - 1 - - - - A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. - pair of interacting organisms of the same species + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity - + - - - - - - - - - - A population which is participating in a migration process. - migratory population + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity - + - + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + + + + + + + + + + + 2 + + + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + A population process during which a population moves from one area to another. @@ -7883,9 +7760,15 @@ Classes for population already exist in IDO ('organism population', I - - Obsolete Class - + + + + + + + + + @@ -8277,12 +8160,6 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - @@ -8292,15 +8169,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - @@ -8313,85 +8181,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -8464,18 +8262,16 @@ Classes for population already exist in IDO ('organism population', I - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -8483,10 +8279,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -8495,12 +8290,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -8513,9 +8321,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -8523,18 +8331,17 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - + + + + @@ -8543,25 +8350,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -8571,17 +8365,29 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -8589,79 +8395,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - + + + @@ -8670,364 +8406,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - + + + @@ -9040,28 +8421,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - + + + @@ -9069,30 +8431,15 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - diff --git a/pco.obo b/pco.obo index 7b026ec..88da0ef 100644 --- a/pco.obo +++ b/pco.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-08-26 +data-version: releases/2021-05-03 remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -32,7 +32,6 @@ name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string @@ -52,7 +51,6 @@ id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity -relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string @@ -74,7 +72,6 @@ def: "b is an independent continuant = Def. b is a continuant which is such that is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -98,7 +95,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl id: BFO:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_obsolete: true [Term] @@ -163,7 +160,6 @@ def: "A continuant that inheres in or is borne by other entities. Every instance def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} @@ -467,31 +463,37 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0007610 ! behavior -is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 -name: interspecies interaction between organisms +name: biological process involved in interspecies interaction between organisms namespace: biological_process -def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] +subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 -name: intraspecies interaction between organisms +name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -1137,8 +1139,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:4751 name: Fungi namespace: ncbi_taxonomy -synonym: "fungi" RELATED blast_name [] synonym: "fungi" RELATED in_part [] +synonym: "fungi" RELATED blast_name [] synonym: "Mycota" RELATED genbank_synonym [] xref: GC_ID:1 xref: PMID:11062127 @@ -1301,10 +1303,6 @@ is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: ObsoleteClass -name: Obsolete Class - [Term] id: PATO:0000001 name: quality @@ -1703,6 +1701,7 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity +intersection_of: BFO:0000027 ! object aggregate intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid @@ -1791,7 +1790,7 @@ property_value: IAO:0000114 IAO:0000123 id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 @@ -1830,21 +1829,21 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 name: obsolete predator role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 name: obsolete prey role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 name: obsolete symbiont role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} @@ -1868,10 +1867,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid -relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1922,7 +1917,7 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000000 ! collection of organisms +is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 @@ -1933,7 +1928,7 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:st id: PCO:0000025 name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1941,7 +1936,7 @@ is_obsolete: true id: PCO:0000026 name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1963,7 +1958,7 @@ id: PCO:0000028 name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1983,7 +1978,7 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_a: PCO:0000024 ! household property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2064,7 +2059,7 @@ def: "An ecological community which is composed primarily of dwarf or short mang synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2074,7 +2069,7 @@ id: PCO:0000041 name: obsolete invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2082,7 +2077,7 @@ is_obsolete: true id: PCO:0000042 name: obsolete microbe synonym: "microbial organism" EXACT [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2090,7 +2085,7 @@ is_obsolete: true id: PCO:0000043 name: obsolete collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2099,7 +2094,7 @@ is_obsolete: true id: PCO:0000044 name: obsolete multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2108,7 +2103,7 @@ is_obsolete: true id: PCO:0000045 name: obsolete single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2118,7 +2113,7 @@ id: PCO:0000046 name: obsolete microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2131,7 +2126,7 @@ synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: part_of ENVO:01001369 ! tidal mangrove shrubland +relationship: BFO:0000050 ENVO:01001369 ! part of tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] @@ -2151,7 +2146,6 @@ is_a: CARO:0001010 ! organism or virus or viroid id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: PCO:0000000 ! collection of organisms intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe relationship: RO:0002351 PCO:0000049 ! has member microbe @@ -2271,12 +2265,109 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 ! mass density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 @@ -2284,7 +2375,7 @@ name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -2348,6 +2439,38 @@ property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "STATO" xsd:string property_value: STATO:0000032 "" xsd:string +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + [Typedef] id: BFO:0000054 name: realized in @@ -2390,7 +2513,6 @@ property_value: IAO:0000118 "preceded_by" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -2404,7 +2526,6 @@ property_value: IAO:0000111 "precedes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2413,6 +2534,9 @@ id: BFO:0000066 name: occurs in def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string @@ -2420,9 +2544,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 +holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 @@ -2444,8 +2568,9 @@ property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosop [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true [Typedef] id: RO:0000052 @@ -2500,7 +2625,6 @@ property_value: IAO:0000118 "has_participant" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000058 @@ -2678,58 +2802,6 @@ property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - [Typedef] id: RO:0002022 name: directly regulated by @@ -2760,18 +2832,6 @@ inverse_of: RO:0002629 ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002086 name: ends after @@ -2808,34 +2868,22 @@ is_a: BFO:0000063 ! precedes id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: has_part RO:0002131 -holds_over_chain: part_of part_of is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: RO:0002211 name: regulates def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2858,6 +2906,9 @@ inverse_of: RO:0002334 ! regulated by id: RO:0002212 name: negatively regulates def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -2871,6 +2922,9 @@ inverse_of: RO:0002335 ! negatively regulated by id: RO:0002213 name: positively regulates def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2898,7 +2952,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] [Typedef] id: RO:0002216 @@ -2908,10 +2961,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002222 @@ -2931,13 +2982,15 @@ range: BFO:0000003 ! occurrent id: RO:0002233 name: has input def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "consumes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -2945,6 +2998,7 @@ inverse_of: RO:0002352 ! input of id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of @@ -2955,6 +3009,7 @@ is_a: RO:0002264 ! acts upstream of or within id: RO:0002264 name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -2966,6 +3021,8 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002411 @@ -3003,6 +3060,7 @@ property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002327 name: enables +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -3015,8 +3073,6 @@ property_value: IAO:0000232 "This relation is currently used experimentally by t property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part -transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3033,7 +3089,6 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "false" xsd:boolean property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3045,15 +3100,14 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 part_of is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0000057 ! has participant @@ -3099,7 +3153,7 @@ property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -3108,7 +3162,7 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -3156,6 +3210,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl id: RO:0002411 name: causally upstream of def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3350,7 +3406,6 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] id: RO:0002481 @@ -3435,6 +3490,9 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002578 name: directly regulates def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3450,7 +3508,6 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: has_part RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3507,6 +3564,9 @@ is_a: RO:0002410 ! causally related to id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3518,6 +3578,9 @@ is_a: RO:0002578 ! directly regulates id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3530,7 +3593,6 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: cjm creation_date: 2018-01-25T23:20:13Z @@ -3538,6 +3600,7 @@ creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect @@ -3549,6 +3612,7 @@ creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 @@ -3560,6 +3624,7 @@ creation_date: 2018-01-26T23:49:51Z id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect @@ -3573,6 +3638,7 @@ creation_date: 2018-01-26T23:53:14Z id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect @@ -3645,29 +3711,6 @@ property_value: IAO:0000119 GROUP:OBI: xsd:s property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true -[Typedef] -id: has_part -name: has part -name: has_part -namespace: external -namespace: quality -def: "a core relation that holds between a whole and its part" [] -def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] -comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. -xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to @@ -3680,38 +3723,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: part_of -name: part of -name: part_of -namespace: external -namespace: quality -def: "a core relation that holds between a part and its whole" [] -xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: has_part ! has part - [Typedef] id: reciprocal_of name: reciprocal_of diff --git a/pco.owl b/pco.owl index fc88485..313a18f 100644 --- a/pco.owl +++ b/pco.owl @@ -17,7 +17,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -132,9 +132,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -161,9 +161,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -227,8 +227,8 @@ We also have the outstanding issue of how to aim different definitions to differ Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -272,6 +272,7 @@ We also have the outstanding issue of how to aim different definitions to differ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item @@ -870,7 +871,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace @@ -919,7 +919,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - shorthand @@ -1031,7 +1030,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - is part of @@ -1046,24 +1044,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - - - - - - - - BFO:0000050 - external - quality - part_of - part_of - - part of part of - part_of - - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1072,13 +1053,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime @@ -1087,23 +1066,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - external - quality - has_part - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part has part - has_part - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - @@ -1152,10 +1116,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -1176,10 +1136,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -1208,6 +1164,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in unfolds in unfolds_in + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in @@ -1248,11 +1207,9 @@ Some currently missing phenomena that should be considered "about" are - - - - - has member of + + obsolete has member of + true @@ -1313,10 +1270,6 @@ Some currently missing phenomena that should be considered "about" are - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -1555,13 +1508,13 @@ Some currently missing phenomena that should be considered "about" are - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. @@ -1603,78 +1556,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -1735,28 +1616,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -1805,56 +1664,16 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -1881,6 +1700,9 @@ Some currently missing phenomena that should be considered "about" are Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false + + + regulates @@ -1898,6 +1720,9 @@ Some currently missing phenomena that should be considered "about" are negatively regulates (process to process) + + + negatively regulates @@ -1920,6 +1745,9 @@ Some currently missing phenomena that should be considered "about" are positively regulates (process to process) + + + positively regulates @@ -1940,7 +1768,6 @@ Some currently missing phenomena that should be considered "about" are For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) capable of @@ -1953,27 +1780,13 @@ Some currently missing phenomena that should be considered "about" are - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of - - - - - - - - true - @@ -2001,11 +1814,13 @@ Some currently missing phenomena that should be considered "about" are - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes + + + has input @@ -2023,6 +1838,7 @@ Some currently missing phenomena that should be considered "about" are A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -2041,6 +1857,7 @@ Some currently missing phenomena that should be considered "about" are A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects + acts upstream of or within @@ -2055,6 +1872,8 @@ Some currently missing phenomena that should be considered "about" are cjm + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2107,14 +1926,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -2124,6 +1935,7 @@ Some currently missing phenomena that should be considered "about" are is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables @@ -2146,25 +1958,12 @@ Some currently missing phenomena that should be considered "about" are - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -2173,14 +1972,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -2199,6 +1990,7 @@ Some currently missing phenomena that should be considered "about" are inverse of enables Chris Mungall + enabled by @@ -2358,6 +2150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall + + causally upstream of @@ -2521,7 +2315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm + GOC:cjm GOC:dos @@ -2664,25 +2458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -2817,6 +2598,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly regulates (processual) + + + directly regulates @@ -2828,10 +2612,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -2928,6 +2708,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates (process to process) + + + directly positively regulates @@ -2943,6 +2726,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates (process to process) + + + directly negatively regulates @@ -2953,10 +2739,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -2977,6 +2759,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:30Z + acts upstream of or within, positive effect @@ -2995,6 +2778,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:51Z + acts upstream of or within, negative effect @@ -3014,6 +2798,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -3034,6 +2819,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -3213,12 +2999,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3303,12 +3083,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3380,12 +3154,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - ic @@ -3410,6 +3178,12 @@ For example, A and B may be gene products and binding of B by A positively regul independent continuant + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + @@ -3440,12 +3214,6 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - @@ -3575,12 +3343,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - sdc SpecificallyDependentContinuant @@ -4145,22 +3907,25 @@ For example, A and B may be gene products and binding of B by A positively regul - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction + interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 + - interspecies interaction between organisms + biological process involved in interspecies interaction between organisms - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. GOC:cc @@ -4171,12 +3936,15 @@ For example, A and B may be gene products and binding of B by A positively regul Any process in which an organism has an effect on an organism of the same species. + https://github.com/geneontology/go-ontology/issues/20191 + intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 + - intraspecies interaction between organisms + biological process involved in intraspecies interaction between organisms @@ -6772,6 +6540,7 @@ No imports + @@ -7084,33 +6853,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -7185,7 +6928,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -7489,7 +7232,6 @@ Classes for population already exist in IDO ('organism population', I - @@ -7732,61 +7474,196 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - 2 - - - - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria - + - - - - - - - 1 - - - - A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. - pair of interacting organisms of the same species + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity - + - - - - - - - - - - A population which is participating in a migration process. - migratory population + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity - + - + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + + + + + + + + + + + 2 + + + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + A population process during which a population moves from one area to another. @@ -7883,9 +7760,15 @@ Classes for population already exist in IDO ('organism population', I - - Obsolete Class - + + + + + + + + + @@ -8277,12 +8160,6 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - @@ -8292,15 +8169,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - @@ -8313,85 +8181,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -8464,18 +8262,16 @@ Classes for population already exist in IDO ('organism population', I - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -8483,10 +8279,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -8495,12 +8290,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -8513,9 +8321,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -8523,18 +8331,17 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - + + + + @@ -8543,25 +8350,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -8571,17 +8365,29 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -8589,79 +8395,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - + + + @@ -8670,364 +8406,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - + + + @@ -9040,28 +8421,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - + + + @@ -9069,30 +8431,15 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - diff --git a/reports/pco-edit.owl-obo-report.tsv b/reports/pco-edit.owl-obo-report.tsv index 02983a2..0d2c93a 100644 --- a/reports/pco-edit.owl-obo-report.tsv +++ b/reports/pco-edit.owl-obo-report.tsv @@ -1,17 +1,18 @@ Level Rule Name Subject Property Value -ERROR missing_label BFO:0000017 rdfs:label -ERROR missing_label ECOCORE:00000045 rdfs:label -ERROR missing_label GO:0051704 rdfs:label -ERROR missing_label IAO:0000030 rdfs:label -ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en -ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en -WARN missing_definition BFO:0000017 IAO:0000115 -WARN missing_definition ECOCORE:00000045 IAO:0000115 -WARN missing_definition GO:0051704 IAO:0000115 -WARN missing_definition IAO:0000030 IAO:0000115 -WARN missing_definition PCO:0000049 IAO:0000115 -WARN missing_definition PCO:0000055 IAO:0000115 -INFO missing_superclass PCO:0000003 rdfs:subClassOf -INFO missing_superclass PCO:0000004 rdfs:subClassOf -INFO missing_superclass PCO:0000050 rdfs:subClassOf -INFO missing_superclass PCO:0000052 rdfs:subClassOf +ERROR missing_label BFO:0000017 rdfs:label +ERROR missing_label ECOCORE:00000045 rdfs:label +ERROR missing_label GO:0051704 rdfs:label +ERROR missing_label IAO:0000030 rdfs:label +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en +WARN missing_definition BFO:0000017 IAO:0000115 +WARN missing_definition ECOCORE:00000045 IAO:0000115 +WARN missing_definition GO:0051704 IAO:0000115 +WARN missing_definition IAO:0000030 IAO:0000115 +WARN missing_definition PCO:0000049 IAO:0000115 +WARN missing_definition PCO:0000077 IAO:0000115 +INFO missing_superclass PCO:0000003 rdfs:subClassOf +INFO missing_superclass PCO:0000004 rdfs:subClassOf +INFO missing_superclass PCO:0000050 rdfs:subClassOf +INFO missing_superclass PCO:0000052 rdfs:subClassOf +INFO missing_superclass PCO:0001000 rdfs:subClassOf diff --git a/src/ontology/Makefile b/src/ontology/Makefile index ad89868..5877ee5 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -58,7 +58,7 @@ $TMPDIR: MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(ONT)-$(r)) $(ONT)) MAIN_GZIPPED = -MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) #$(MAIN_GZIPPED) all_main: $(MAIN_FILES) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 9fb8d25..f099a94 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -11,17 +11,24 @@ - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/imports/pato_import.obo b/src/ontology/imports/pato_import.obo index 8dc42b7..637a537 100644 --- a/src/ontology/imports/pato_import.obo +++ b/src/ontology/imports/pato_import.obo @@ -1,5 +1,5 @@ format-version: 1.2 -ontology: pco/imports/pato_import +ontology: pco/imports/pato_import.obo owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: ()\n\nSubClassOf( ObjectHasSelf())\n\n\nSubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nSubObjectPropertyOf(ObjectPropertyChain( ) )\nDLSafeRule(Annotation( \"true\"^^xsd:boolean) Annotation(rdfs:comment \"MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z\"^^xsd:string) Annotation(rdfs:label \"infer input from direct reg\"^^xsd:string) Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Annotation(rdfs:label \"'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).\") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nDLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable())))\nAnnotationAssertion(rdfs:comment \"\")\n) [Term] diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 8aca225..eaa5967 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -415,87 +415,6 @@ - - - - - - - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) - a core relation that holds between a part and its whole - Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - - BFO:0000050 - external - quality - part_of - - - - - part_of - - part of - - - http://www.obofoundry.org/ro/#OBO_REL:part_of - - - - - - - - - - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - a core relation that holds between a whole and its part - Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. - Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime - Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - - BFO:0000051 - external - quality - - - - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part - - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - - - - @@ -504,10 +423,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -528,10 +443,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -547,14 +458,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in @@ -605,10 +508,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -623,78 +522,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -755,27 +582,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -824,22 +630,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) @@ -850,32 +640,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -887,10 +651,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - @@ -986,10 +746,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in @@ -997,15 +753,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. capable of part of - - - - - - - - true - @@ -1132,14 +879,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -1172,25 +911,12 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -1199,14 +925,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -1664,25 +1382,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -1831,10 +1536,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -1962,10 +1663,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -2193,19 +1890,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant @@ -2216,18 +1901,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - An entity that has temporal parts and that happens, unfolds or develops through time. occurrent @@ -2239,12 +1912,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. @@ -2268,12 +1935,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant @@ -3274,12 +2935,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - @@ -3289,15 +2944,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - @@ -3310,85 +2956,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -3460,124 +3036,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -3647,451 +3105,6 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). diff --git a/src/ontology/pco-base.obo b/src/ontology/pco-base.obo index 89d34f8..19cf037 100644 --- a/src/ontology/pco-base.obo +++ b/src/ontology/pco-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/pco-base.owl +data-version: pco/releases/2021-05-03/pco-base.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-base property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -60,7 +60,7 @@ id: PCO:0000000 name: collection of organisms def: "A material entity that consists of two or more organisms, viruses, or viroids." [] comment: May be of the same or different species. -is_a: BFO:0000027 +intersection_of: BFO:0000027 intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! organism or virus or viroid @@ -221,9 +221,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! organism or virus or viroid property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -617,19 +614,116 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: IAO:0000116 "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] -is_a: BFO:0000040 -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! organism or virus or viroid [Term] id: PCO:0001001 name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] +is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -682,6 +776,7 @@ property_value: IAO:0000119 http://dx.doi.org/10.1038/ismej.2009.88 xsd:string [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true diff --git a/src/ontology/pco-base.owl b/src/ontology/pco-base.owl index d554572..0e81848 100644 --- a/src/ontology/pco-base.owl +++ b/src/ontology/pco-base.owl @@ -11,7 +11,7 @@ xmlns:terms="http://purl.org/dc/terms/" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -146,6 +146,12 @@ + + + + + + @@ -184,11 +190,9 @@ - - - - - has member of + + obsolete has member of + true @@ -390,6 +394,12 @@ + + + + + + @@ -414,6 +424,7 @@ + @@ -426,7 +437,6 @@ - @@ -705,26 +715,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. @@ -1326,17 +1316,157 @@ Classes for population already exist in IDO ('organism population', I + + + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria + + + + + + + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity + + + + + + + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity + + + + + + + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + - - - - - 2 - - - + + + + + + + 2 + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. pair of interacting organisms @@ -1346,14 +1476,9 @@ Classes for population already exist in IDO ('organism population', I + - - - - 1 - - - + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. pair of interacting organisms of the same species diff --git a/src/ontology/pco-edit.owl b/src/ontology/pco-edit.owl index e54f4fb..97adbdd 100644 --- a/src/ontology/pco-edit.owl +++ b/src/ontology/pco-edit.owl @@ -6,9 +6,9 @@ @prefix xml: . @prefix xsd: . @prefix rdfs: . -@base . +@base . - rdf:type owl:Ontology ; + rdf:type owl:Ontology ; owl:imports , , , diff --git a/src/ontology/pco-full.obo b/src/ontology/pco-full.obo index 08e5f17..414bee3 100644 --- a/src/ontology/pco-full.obo +++ b/src/ontology/pco-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: pco/releases/2020-08-26/pco-full.owl +data-version: pco/releases/2021-05-03/pco-full.owl remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco/pco-full property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -32,7 +32,6 @@ name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string @@ -52,7 +51,6 @@ id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity -relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string @@ -74,7 +72,6 @@ def: "b is an independent continuant = Def. b is a continuant which is such that is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -98,7 +95,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl id: BFO:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_obsolete: true [Term] @@ -163,7 +160,6 @@ def: "A continuant that inheres in or is borne by other entities. Every instance def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} @@ -467,31 +463,37 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0007610 ! behavior -is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 -name: interspecies interaction between organisms +name: biological process involved in interspecies interaction between organisms namespace: biological_process -def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] +subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 -name: intraspecies interaction between organisms +name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -1301,10 +1303,6 @@ is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: ObsoleteClass -name: Obsolete Class - [Term] id: PATO:0000001 name: quality @@ -1703,6 +1701,7 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity +intersection_of: BFO:0000027 ! object aggregate intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid @@ -1791,7 +1790,7 @@ property_value: IAO:0000114 IAO:0000123 id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 @@ -1830,21 +1829,21 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 name: obsolete predator role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 name: obsolete prey role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 name: obsolete symbiont role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} @@ -1868,10 +1867,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid -relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1922,7 +1917,7 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000000 ! collection of organisms +is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 @@ -1933,7 +1928,7 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:st id: PCO:0000025 name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1941,7 +1936,7 @@ is_obsolete: true id: PCO:0000026 name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1963,7 +1958,7 @@ id: PCO:0000028 name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1983,7 +1978,7 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_a: PCO:0000024 ! household property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2064,7 +2059,7 @@ def: "An ecological community which is composed primarily of dwarf or short mang synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2074,7 +2069,7 @@ id: PCO:0000041 name: obsolete invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2082,7 +2077,7 @@ is_obsolete: true id: PCO:0000042 name: obsolete microbe synonym: "microbial organism" EXACT [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2090,7 +2085,7 @@ is_obsolete: true id: PCO:0000043 name: obsolete collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2099,7 +2094,7 @@ is_obsolete: true id: PCO:0000044 name: obsolete multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2108,7 +2103,7 @@ is_obsolete: true id: PCO:0000045 name: obsolete single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2118,7 +2113,7 @@ id: PCO:0000046 name: obsolete microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2131,7 +2126,7 @@ synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: part_of ENVO:01001369 ! tidal mangrove shrubland +relationship: BFO:0000050 ENVO:01001369 ! part of tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] @@ -2151,7 +2146,6 @@ is_a: CARO:0001010 ! organism or virus or viroid id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: PCO:0000000 ! collection of organisms intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe relationship: RO:0002351 PCO:0000049 ! has member microbe @@ -2271,12 +2265,109 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 ! mass density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 @@ -2284,7 +2375,7 @@ name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -2348,6 +2439,38 @@ property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "STATO" xsd:string property_value: STATO:0000032 "" xsd:string +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + [Typedef] id: BFO:0000054 name: realized in @@ -2390,7 +2513,6 @@ property_value: IAO:0000118 "preceded_by" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -2404,7 +2526,6 @@ property_value: IAO:0000111 "precedes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2413,6 +2534,9 @@ id: BFO:0000066 name: occurs in def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string @@ -2420,9 +2544,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 +holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 @@ -2444,8 +2568,9 @@ property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosop [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true [Typedef] id: RO:0000052 @@ -2500,7 +2625,6 @@ property_value: IAO:0000118 "has_participant" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000058 @@ -2678,58 +2802,6 @@ property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - [Typedef] id: RO:0002022 name: directly regulated by @@ -2760,18 +2832,6 @@ inverse_of: RO:0002629 ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002086 name: ends after @@ -2808,34 +2868,22 @@ is_a: BFO:0000063 ! precedes id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: has_part RO:0002131 -holds_over_chain: part_of part_of is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: RO:0002211 name: regulates def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2858,6 +2906,9 @@ inverse_of: RO:0002334 ! regulated by id: RO:0002212 name: negatively regulates def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -2871,6 +2922,9 @@ inverse_of: RO:0002335 ! negatively regulated by id: RO:0002213 name: positively regulates def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2898,7 +2952,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] [Typedef] id: RO:0002216 @@ -2908,10 +2961,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002222 @@ -2931,13 +2982,15 @@ range: BFO:0000003 ! occurrent id: RO:0002233 name: has input def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "consumes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -2945,6 +2998,7 @@ inverse_of: RO:0002352 ! input of id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of @@ -2955,6 +3009,7 @@ is_a: RO:0002264 ! acts upstream of or within id: RO:0002264 name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -2966,6 +3021,8 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002411 @@ -3003,6 +3060,7 @@ property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002327 name: enables +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -3015,8 +3073,6 @@ property_value: IAO:0000232 "This relation is currently used experimentally by t property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part -transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3033,7 +3089,6 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "false" xsd:boolean property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3045,15 +3100,14 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 part_of is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0000057 ! has participant @@ -3099,7 +3153,7 @@ property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -3108,7 +3162,7 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -3156,6 +3210,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl id: RO:0002411 name: causally upstream of def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3350,7 +3406,6 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] id: RO:0002481 @@ -3435,6 +3490,9 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002578 name: directly regulates def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3450,7 +3508,6 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: has_part RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3507,6 +3564,9 @@ is_a: RO:0002410 ! causally related to id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3518,6 +3578,9 @@ is_a: RO:0002578 ! directly regulates id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3530,7 +3593,6 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: cjm creation_date: 2018-01-25T23:20:13Z @@ -3538,6 +3600,7 @@ creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect @@ -3549,6 +3612,7 @@ creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 @@ -3560,6 +3624,7 @@ creation_date: 2018-01-26T23:49:51Z id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect @@ -3573,6 +3638,7 @@ creation_date: 2018-01-26T23:53:14Z id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect @@ -3645,29 +3711,6 @@ property_value: IAO:0000119 GROUP:OBI: xsd:s property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true -[Typedef] -id: has_part -name: has part -name: has_part -namespace: external -namespace: quality -def: "a core relation that holds between a whole and its part" [] -def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] -comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. -xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to @@ -3680,38 +3723,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: part_of -name: part of -name: part_of -namespace: external -namespace: quality -def: "a core relation that holds between a part and its whole" [] -xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: has_part ! has part - [Typedef] id: reciprocal_of name: reciprocal_of diff --git a/src/ontology/pco-full.owl b/src/ontology/pco-full.owl index b73706e..a8b8623 100644 --- a/src/ontology/pco-full.owl +++ b/src/ontology/pco-full.owl @@ -17,7 +17,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -132,9 +132,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -161,9 +161,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -227,8 +227,8 @@ We also have the outstanding issue of how to aim different definitions to differ Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -272,6 +272,7 @@ We also have the outstanding issue of how to aim different definitions to differ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item @@ -870,7 +871,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace @@ -919,7 +919,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - shorthand @@ -1031,7 +1030,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - is part of @@ -1046,24 +1044,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - - - - - - - - BFO:0000050 - external - quality - part_of - part_of - - part of part of - part_of - - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1072,13 +1053,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime @@ -1087,23 +1066,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - external - quality - has_part - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part has part - has_part - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - @@ -1152,10 +1116,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -1176,10 +1136,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -1208,6 +1164,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in unfolds in unfolds_in + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in @@ -1248,11 +1207,9 @@ Some currently missing phenomena that should be considered "about" are - - - - - has member of + + obsolete has member of + true @@ -1313,10 +1270,6 @@ Some currently missing phenomena that should be considered "about" are - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -1555,13 +1508,13 @@ Some currently missing phenomena that should be considered "about" are - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. @@ -1603,78 +1556,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -1735,28 +1616,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -1805,56 +1664,16 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -1881,6 +1700,9 @@ Some currently missing phenomena that should be considered "about" are Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false + + + regulates @@ -1898,6 +1720,9 @@ Some currently missing phenomena that should be considered "about" are negatively regulates (process to process) + + + negatively regulates @@ -1920,6 +1745,9 @@ Some currently missing phenomena that should be considered "about" are positively regulates (process to process) + + + positively regulates @@ -1940,7 +1768,6 @@ Some currently missing phenomena that should be considered "about" are For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) capable of @@ -1953,27 +1780,13 @@ Some currently missing phenomena that should be considered "about" are - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of - - - - - - - - true - @@ -2001,11 +1814,13 @@ Some currently missing phenomena that should be considered "about" are - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes + + + has input @@ -2023,6 +1838,7 @@ Some currently missing phenomena that should be considered "about" are A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -2041,6 +1857,7 @@ Some currently missing phenomena that should be considered "about" are A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects + acts upstream of or within @@ -2055,6 +1872,8 @@ Some currently missing phenomena that should be considered "about" are cjm + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2107,14 +1926,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -2124,6 +1935,7 @@ Some currently missing phenomena that should be considered "about" are is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables @@ -2146,25 +1958,12 @@ Some currently missing phenomena that should be considered "about" are - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -2173,14 +1972,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -2199,6 +1990,7 @@ Some currently missing phenomena that should be considered "about" are inverse of enables Chris Mungall + enabled by @@ -2358,6 +2150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall + + causally upstream of @@ -2521,7 +2315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm + GOC:cjm GOC:dos @@ -2664,25 +2458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -2817,6 +2598,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly regulates (processual) + + + directly regulates @@ -2828,10 +2612,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -2928,6 +2708,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates (process to process) + + + directly positively regulates @@ -2943,6 +2726,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates (process to process) + + + directly negatively regulates @@ -2953,10 +2739,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -2977,6 +2759,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:30Z + acts upstream of or within, positive effect @@ -2995,6 +2778,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:51Z + acts upstream of or within, negative effect @@ -3014,6 +2798,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -3034,6 +2819,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -3213,12 +2999,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3303,12 +3083,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3380,12 +3154,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - ic @@ -3410,6 +3178,12 @@ For example, A and B may be gene products and binding of B by A positively regul independent continuant + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + @@ -3440,12 +3214,6 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - @@ -3575,12 +3343,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - sdc SpecificallyDependentContinuant @@ -4145,22 +3907,25 @@ For example, A and B may be gene products and binding of B by A positively regul - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction + interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 + - interspecies interaction between organisms + biological process involved in interspecies interaction between organisms - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. GOC:cc @@ -4171,12 +3936,15 @@ For example, A and B may be gene products and binding of B by A positively regul Any process in which an organism has an effect on an organism of the same species. + https://github.com/geneontology/go-ontology/issues/20191 + intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 + - intraspecies interaction between organisms + biological process involved in intraspecies interaction between organisms @@ -6772,6 +6540,7 @@ No imports + @@ -7084,33 +6853,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -7185,7 +6928,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -7489,7 +7232,6 @@ Classes for population already exist in IDO ('organism population', I - @@ -7732,61 +7474,196 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - 2 - - - - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria - + - - - - - - - 1 - - - - A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. - pair of interacting organisms of the same species + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity - + - - - - - - - - - - A population which is participating in a migration process. - migratory population + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity - + - + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + + + + + + + + + + + 2 + + + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + A population process during which a population moves from one area to another. @@ -7883,9 +7760,15 @@ Classes for population already exist in IDO ('organism population', I - - Obsolete Class - + + + + + + + + + @@ -8277,12 +8160,6 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - @@ -8292,15 +8169,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - @@ -8313,85 +8181,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -8464,18 +8262,16 @@ Classes for population already exist in IDO ('organism population', I - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -8483,10 +8279,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -8495,12 +8290,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -8513,9 +8321,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -8523,18 +8331,17 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - + + + + @@ -8543,25 +8350,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -8571,17 +8365,29 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -8589,79 +8395,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - + + + @@ -8670,364 +8406,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - + + + @@ -9040,28 +8421,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - + + + @@ -9069,30 +8431,15 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - diff --git a/src/ontology/pco.obo b/src/ontology/pco.obo index 7b026ec..88da0ef 100644 --- a/src/ontology/pco.obo +++ b/src/ontology/pco.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2020-08-26 +data-version: releases/2021-05-03 remark: The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. ontology: pco property_value: http://purl.org/dc/elements/1.1/contributor http://orcid.org/0000-0002-4366-3088 xsd:string @@ -32,7 +32,6 @@ name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent -relationship: part_of BFO:0000002 ! continuant property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: editor_note "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string @@ -52,7 +51,6 @@ id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity -relationship: part_of BFO:0000003 ! occurrent property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: editor_note "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string @@ -74,7 +72,6 @@ def: "b is an independent continuant = Def. b is a continuant which is such that is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000004 ! independent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string @@ -98,7 +95,7 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl id: BFO:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_obsolete: true [Term] @@ -163,7 +160,6 @@ def: "A continuant that inheres in or is borne by other entities. Every instance def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant -relationship: part_of BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: editor_note "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} @@ -467,31 +463,37 @@ synonym: "cooperative behavior" RELATED [] synonym: "social behaviour" EXACT [] xref: Wikipedia:Social_behavior is_a: GO:0007610 ! behavior -is_a: GO:0051703 ! intraspecies interaction between organisms +is_a: GO:0051703 ! biological process involved in intraspecies interaction between organisms property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044419 -name: interspecies interaction between organisms +name: biological process involved in interspecies interaction between organisms namespace: biological_process -def: "Any process in which an organism has an effect on an organism of a different species." [GOC:cc] +def: "Any process evolved to enable an interaction with an organism of a different species." [GOC:cc] +subset: gocheck_do_not_annotate subset: goslim_candida subset: goslim_pir synonym: "interaction with another species" EXACT [] synonym: "interspecies interaction" EXACT [] +synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0051703 -name: intraspecies interaction between organisms +name: biological process involved in intraspecies interaction between organisms namespace: biological_process def: "Any process in which an organism has an effect on an organism of the same species." [GOC:ai] +subset: gocheck_do_not_annotate subset: goslim_pir +synonym: "intraspecies interaction between organisms" EXACT [] synonym: "intraspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process +property_value: IAO:0000233 https://github.com/geneontology/go-ontology/issues/20191 xsd:anyURI property_value: isDefinedBy http://purl.obolibrary.org/obo/go.owl [Term] @@ -1137,8 +1139,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl id: NCBITaxon:4751 name: Fungi namespace: ncbi_taxonomy -synonym: "fungi" RELATED blast_name [] synonym: "fungi" RELATED in_part [] +synonym: "fungi" RELATED blast_name [] synonym: "Mycota" RELATED genbank_synonym [] xref: GC_ID:1 xref: PMID:11062127 @@ -1301,10 +1303,6 @@ is_a: NCBITaxon:9605 ! Homo property_value: has_rank NCBITaxon:species property_value: isDefinedBy http://purl.obolibrary.org/obo/ncbitaxon.owl -[Term] -id: ObsoleteClass -name: Obsolete Class - [Term] id: PATO:0000001 name: quality @@ -1703,6 +1701,7 @@ def: "A material entity that consists of two or more organisms, viruses, or viro comment: May be of the same or different species. is_a: BFO:0000027 ! object aggregate is_a: PCO:0000031 ! organismal entity +intersection_of: BFO:0000027 ! object aggregate intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid relationship: RO:0002351 CARO:0001010 ! has member organism or virus or viroid @@ -1791,7 +1790,7 @@ property_value: IAO:0000114 IAO:0000123 id: PCO:0000009 name: obsolete carrying capacity def: "The maximum number of individuals that can be supported in a population that is growing according to logistic growth." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Carrying capacity is better defined as a quality of the environment in which a population lives. This term will be deprecated from PCO and moved to ecoCORE." xsd:string property_value: IAO:0000119 ISBN:0878932739 xsd:string property_value: IAO:0000231 IAO:0000423 @@ -1830,21 +1829,21 @@ property_value: IAO:0000114 IAO:0000123 [Term] id: PCO:0000014 name: obsolete predator role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000015 name: obsolete prey role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} [Term] id: PCO:0000016 name: obsolete symbiont role -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Interactions are now covered in EcoCore ontology." xsd:string is_obsolete: true {http://purl.obolibrary.org/obo/IAO_0000231="IAO:0000103"} @@ -1868,10 +1867,6 @@ id: PCO:0000018 name: single-species collection of organisms def: "A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species." [] is_a: PCO:0000000 ! collection of organisms -intersection_of: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms -intersection_of: RO:0002351 CARO:0001010 {all_only="true"} ! has member organism or virus or viroid -intersection_of: RO:0002351 CARO:0001010 {minCardinality="2"} ! has member organism or virus or viroid -relationship: PCO:0000055 PCO:0000017 ! has member of species as a collection of organisms property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000118 "collection of organisms of the same species" xsd:string @@ -1922,7 +1917,7 @@ property_value: IAO:0000119 "adapted from http://en.wikipedia.org/wiki/Species_e id: PCO:0000024 name: household def: "An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people." [] -is_a: PCO:0000000 ! collection of organisms +is_a: PCO:0000031 ! organismal entity relationship: RO:0002321 ENVO:01000744 ! ecologically related to human dwelling relationship: RO:0002351 NCBITaxon:9606 {minCardinality="1"} ! has member Homo sapiens property_value: IAO:0000114 IAO:0000123 @@ -1933,7 +1928,7 @@ property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Household" xsd:st id: PCO:0000025 name: obsolete red population comment: This is an example population added to demonstrate the modeling pattern for collections of organisms. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1941,7 +1936,7 @@ is_obsolete: true id: PCO:0000026 name: obsolete red organism comment: An example class added to demonstrate the design pattern for collections of organism. Red organism should be automatically classified as a member of red population when the reasoner is synchronized using a DL query. -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000002 is_obsolete: true @@ -1963,7 +1958,7 @@ id: PCO:0000028 name: obsolete community def: "A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other." [] comment: These relations can include shared values, occupying the same spatial regkion. A community be be a single species collection of organsisms (as in a human community, which is also a type of population) or a or multi-species collection of organisms (as in an ecological community). -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: editor_note "Biological or social relations are covered by RO_0002437 (biotically interacts with), but that relations does provide an easy way to specify that two entities are interacting with each other (participating in the same interaction). Until that axiom is specified, the logical definition of this term is incomplete." xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -1983,7 +1978,7 @@ name: agricultural household name: obsolete organismal entity def: "A household in which the majority of the income of its members is derived from agricultural activities." [] def: "A material entity that is one or more organisms, viruses or viroids." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass is_a: PCO:0000024 ! household property_value: editor_note "This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term." xsd:string property_value: IAO:0000114 IAO:0000123 @@ -2064,7 +2059,7 @@ def: "An ecological community which is composed primarily of dwarf or short mang synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2074,7 +2069,7 @@ id: PCO:0000041 name: obsolete invisible to unaided eye def: "A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye." [] comment: should move to PATO -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2082,7 +2077,7 @@ is_obsolete: true id: PCO:0000042 name: obsolete microbe synonym: "microbial organism" EXACT [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2090,7 +2085,7 @@ is_obsolete: true id: PCO:0000043 name: obsolete collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2099,7 +2094,7 @@ is_obsolete: true id: PCO:0000044 name: obsolete multi-species collection of microbes def: "A multi-species collection of organisms that consists of two or more microbes from at least two species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2108,7 +2103,7 @@ is_obsolete: true id: PCO:0000045 name: obsolete single species collection of microbes def: "A single-species collection of organisms that consists of two or more microbes of the same species and no members of any other species." [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2118,7 +2113,7 @@ id: PCO:0000046 name: obsolete microbial population def: "A population of organisms consisting of only microbes of the same species, that live in the same place." [] synonym: "microbiota" BROAD [] -is_a: ObsoleteClass ! Obsolete Class +is_a: ObsoleteClass property_value: http://purl.org/dc/elements/1.1/creator https://orcid.org/0000-0001-8815-0078 xsd:string property_value: IAO:0000231 IAO:0000103 is_obsolete: true @@ -2131,7 +2126,7 @@ synonym: "mangrove community" RELATED [] synonym: "tidal shrubland community" RELATED [] xref: https://cmecscatalog.org/cmecs/classification/unit/577.html is_a: PCO:0000002 ! ecological community -relationship: part_of ENVO:01001369 ! tidal mangrove shrubland +relationship: BFO:0000050 ENVO:01001369 ! part of tidal mangrove shrubland property_value: http://purl.org/dc/elements/1.1/contributor https://orcid.org/0000-0002-4366-3088 xsd:string [Term] @@ -2151,7 +2146,6 @@ is_a: CARO:0001010 ! organism or virus or viroid id: PCO:0000050 name: collection of microbial organisms def: "A collection of organisms consisting of two or more microbes." [] -is_a: PCO:0000000 ! collection of organisms intersection_of: RO:0002351 PCO:0000049 {all_only="true"} ! has member microbe intersection_of: RO:0002351 PCO:0000049 {minCardinality="2"} ! has member microbe relationship: RO:0002351 PCO:0000049 ! has member microbe @@ -2271,12 +2265,109 @@ property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000119 http://www.tiem.utk.edu/~gross/bioed/bealsmodules/simpsonDI.html property_value: IAO:0000119 "Inverse_Simpson_index" +[Term] +id: PCO:0000073 +name: alga excluding Cyanobacteria +def: "An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp." [] +synonym: "alga" EXACT [] +synonym: "algae" EXACT [] +synonym: "seaweed" NARROW [] +is_a: CARO:0010004 ! organism +property_value: IAO:0000119 https://en.wikipedia.org/wiki/Algae + +[Term] +id: PCO:0000074 +name: alpha diversity +def: "A community species diversity that is the mean species diversity at a site or within a specific habitat." [] +synonym: "α-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Alpha:diversity + +[Term] +id: PCO:0000075 +name: beta diversity +def: "A community species diversity that is the ratio between regional and local species diversity." [] +synonym: "true beta diversity" EXACT [] +synonym: "β-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Beta:diversity + +[Term] +id: PCO:0000076 +name: gamma diversity +def: "A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity." [] +synonym: "γ-diversity" EXACT [] +is_a: PCO:0000019 ! community species diversity +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000119 Gamma:diversity + +[Term] +id: PCO:0000077 +name: plant density +is_a: PATO:0001019 ! mass density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 +property_value: IAO:0000117 "The density of plants in an ecological community or population, often measured as the number of plants per area." xsd:string + +[Term] +id: PCO:0000078 +name: seedling density +def: "The density of seedlings in an ecological community or population, often measured as the number of seedlings per area." [] +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000079 +name: plant density of a population +def: "The density of plants in a population or organisms (a single species), often measured as the number of plants per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000080 +name: plant density of an ecological community +def: "The density of plants in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000077 ! plant density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000081 +name: seedling density of a population +def: "The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area." [] +is_a: PCO:0000003 ! quality of a population +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + +[Term] +id: PCO:0000082 +name: seedling density of an ecological community +def: "The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area." [] +is_a: PCO:0000004 ! quality of an ecological community +is_a: PCO:0000078 ! seedling density +property_value: editor_note "TBD: add logical definition" xsd:string +property_value: IAO:0000117 https://orcid.org/0000-0001-6284-4821 +property_value: IAO:0000117 https://orcid.org/0000-0001-8815-0078 + [Term] id: PCO:0001000 name: pair of interacting organisms def: "A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other." [] is_a: PCO:0000000 ! collection of organisms -relationship: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid +intersection_of: PCO:0000000 ! collection of organisms +intersection_of: RO:0002351 CARO:0001010 {cardinality="2"} ! has member organism or virus or viroid [Term] id: PCO:0001001 @@ -2284,7 +2375,7 @@ name: pair of interacting organisms of the same species def: "A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other." [] is_a: PCO:0000018 ! single-species collection of organisms is_a: PCO:0001000 ! pair of interacting organisms -relationship: PCO:0000055 PCO:0000017 {cardinality="1"} ! has member of species as a collection of organisms +property_value: IAO:0000114 IAO:0000428 [Term] id: PCO:1000000 @@ -2348,6 +2439,38 @@ property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "STATO" xsd:string property_value: STATO:0000032 "" xsd:string +[Typedef] +id: BFO:0000050 +name: part of +def: "a core relation that holds between a part and its whole" [] +property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string +property_value: IAO:0000111 "is part of" xsd:string +property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string +property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string +property_value: IAO:0000118 "part_of" xsd:string +property_value: RO:0001900 RO:0001901 +property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string +is_transitive: true +inverse_of: BFO:0000051 ! has part + +[Typedef] +id: BFO:0000051 +name: has part +def: "a core relation that holds between a whole and its part" [] +property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string +property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string +property_value: IAO:0000111 "has part" xsd:string +property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string +property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string +property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string +property_value: IAO:0000118 "has_part" xsd:string +property_value: RO:0001900 RO:0001901 +is_transitive: true + [Typedef] id: BFO:0000054 name: realized in @@ -2390,7 +2513,6 @@ property_value: IAO:0000118 "preceded_by" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000062 is_transitive: true is_a: RO:0002086 ! ends after inverse_of: BFO:0000063 ! precedes @@ -2404,7 +2526,6 @@ property_value: IAO:0000111 "precedes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent -holds_over_chain: part_of BFO:0000063 is_transitive: true is_a: RO:0002222 ! temporally related to @@ -2413,6 +2534,9 @@ id: BFO:0000066 name: occurs in def: "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000111 "occurs in" xsd:string property_value: IAO:0000118 "occurs_in" xsd:string property_value: IAO:0000118 "unfolds in" xsd:string @@ -2420,9 +2544,9 @@ property_value: IAO:0000118 "unfolds_in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: part_of BFO:0000066 +holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process -transitive_over: part_of ! part_of +transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 @@ -2444,8 +2568,9 @@ property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosop [Typedef] id: PCO:0000055 -name: has member of -domain: PCO:0000000 ! collection of organisms +name: obsolete has member of +property_value: IAO:0000231 IAO:0000103 +is_obsolete: true [Typedef] id: RO:0000052 @@ -2500,7 +2625,6 @@ property_value: IAO:0000118 "has_participant" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant -holds_over_chain: has_part RO:0000057 [Typedef] id: RO:0000058 @@ -2678,58 +2802,6 @@ property_value: RO:0001900 RO:0001901 domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity -[Typedef] -id: RO:0002013 -name: has regulatory component activity -def: "A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002017 ! has component activity -is_a: RO:0002334 ! regulated by -created_by: dos -creation_date: 2017-05-24T09:30:46Z - -[Typedef] -id: RO:0002014 -name: has negative regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002335 ! negatively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:01Z - -[Typedef] -id: RO:0002015 -name: has positive regulatory component activity -def: "A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B." [] -comment: By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002013 ! has regulatory component activity -is_a: RO:0002336 ! positively regulated by -created_by: dos -creation_date: 2017-05-24T09:31:17Z - -[Typedef] -id: RO:0002017 -name: has component activity -comment: A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_a: RO:0002018 ! has component process -created_by: dos -creation_date: 2017-05-24T09:44:33Z - -[Typedef] -id: RO:0002018 -name: has component process -def: "w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -domain: BFO:0000015 ! process -range: BFO:0000015 ! process -is_a: RO:0002180 ! has component -created_by: dos -creation_date: 2017-05-24T09:49:21Z - [Typedef] id: RO:0002022 name: directly regulated by @@ -2760,18 +2832,6 @@ inverse_of: RO:0002629 ! directly positively regulates created_by: dos creation_date: 2017-09-17T13:52:47Z -[Typedef] -id: RO:0002025 -name: has effector activity -def: "A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity." [GOC:dos] -comment: This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -is_functional: true -is_a: RO:0002017 ! has component activity -is_a: RO:0002211 ! regulates -created_by: dos -creation_date: 2017-09-22T14:14:36Z - [Typedef] id: RO:0002086 name: ends after @@ -2808,34 +2868,22 @@ is_a: BFO:0000063 ! precedes id: RO:0002131 name: overlaps def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0001900 RO:0001901 -holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} -holds_over_chain: has_part RO:0002131 -holds_over_chain: part_of part_of is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] -[Typedef] -id: RO:0002180 -name: has component -def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] -subset: ro-eco -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -property_value: RO:0001900 RO:0001901 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency -is_a: has_part ! has part - [Typedef] id: RO:0002211 name: regulates def: "process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: editor_note "We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string @@ -2858,6 +2906,9 @@ inverse_of: RO:0002334 ! regulated by id: RO:0002212 name: negatively regulates def: "Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string @@ -2871,6 +2922,9 @@ inverse_of: RO:0002335 ! negatively regulated by id: RO:0002213 name: positively regulates def: "Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "positively regulates (process to process)" xsd:string @@ -2898,7 +2952,6 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: RO:0002216 ! capable of part of -expand_expression_to: "RO_0000053 some (RO_0000054 only ?Y)" [] [Typedef] id: RO:0002216 @@ -2908,10 +2961,8 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "has function in" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso "defining-property-chains-involving-reflexivity" -holds_over_chain: RO:0002215 part_of {http://purl.obolibrary.org/obo/RO_0002582="true"} is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process -expand_expression_to: "RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002222 @@ -2931,13 +2982,15 @@ range: BFO:0000003 ! occurrent id: RO:0002233 name: has input def: "p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "consumes" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000015 ! process -range: BFO:0000040 ! material entity is_a: RO:0000057 ! has participant inverse_of: RO:0002352 ! input of @@ -2945,6 +2998,7 @@ inverse_of: RO:0002352 ! input of id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of @@ -2955,6 +3009,7 @@ is_a: RO:0002264 ! acts upstream of or within id: RO:0002264 name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -2966,6 +3021,8 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002304 name: causally upstream of, positive effect comment: holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: http://purl.org/dc/terms/creator "cjm" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002411 @@ -3003,6 +3060,7 @@ property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002327 name: enables +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "catalyzes" xsd:string @@ -3015,8 +3073,6 @@ property_value: IAO:0000232 "This relation is currently used experimentally by t property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0002215 ! capable of inverse_of: RO:0002333 ! enabled by -transitive_over: has_part ! has part -transitive_over: RO:0002017 ! has component activity [Typedef] id: RO:0002328 @@ -3033,7 +3089,6 @@ def: "this relation holds between c and p when c is part of some c', and c' is c property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000118 "false" xsd:boolean property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: part_of RO:0002215 {http://purl.obolibrary.org/obo/RO_0002581="true"} is_a: RO:0002328 ! functionally related to [Typedef] @@ -3045,15 +3100,14 @@ property_value: IAO:0000118 "actively involved in" xsd:string property_value: IAO:0000118 "enables part of" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: seeAlso Involved:in -holds_over_chain: RO:0002327 part_of is_a: RO:0000056 ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl is_a: RO:0000057 ! has participant @@ -3099,7 +3153,7 @@ property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of +is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] @@ -3108,7 +3162,7 @@ name: has member def: "has member is a mereological relation between a collection and an item." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part +is_a: BFO:0000051 ! has part [Typedef] id: RO:0002352 @@ -3156,6 +3210,8 @@ property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl id: RO:0002411 name: causally upstream of def: "p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000114 IAO:0000428 property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3350,7 +3406,6 @@ property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part BFO:0000066 {http://purl.obolibrary.org/obo/RO_0002581="true"} [Typedef] id: RO:0002481 @@ -3435,6 +3490,9 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002578 name: directly regulates def: "Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly regulates (processual)" xsd:string @@ -3450,7 +3508,6 @@ def: "s 'has part structure that is capable of' p if and only if there exists so property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: has_part RO:0002215 is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process @@ -3507,6 +3564,9 @@ is_a: RO:0002410 ! causally related to id: RO:0002629 name: directly positively regulates def: "Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3518,6 +3578,9 @@ is_a: RO:0002578 ! directly regulates id: RO:0002630 name: directly negatively regulates def: "Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl @@ -3530,7 +3593,6 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl -holds_over_chain: RO:0002327 has_part is_a: RO:0002328 ! functionally related to created_by: cjm creation_date: 2018-01-25T23:20:13Z @@ -3538,6 +3600,7 @@ creation_date: 2018-01-25T23:20:13Z [Typedef] id: RO:0004032 name: acts upstream of or within, positive effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002264 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of_or_within,_positive_effect @@ -3549,6 +3612,7 @@ creation_date: 2018-01-26T23:49:30Z [Typedef] id: RO:0004033 name: acts upstream of or within, negative effect +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002264 holds_over_chain: RO:0002327 RO:0004046 @@ -3560,6 +3624,7 @@ creation_date: 2018-01-26T23:49:51Z id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004049 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_positive_effect @@ -3573,6 +3638,7 @@ creation_date: 2018-01-26T23:53:14Z id: RO:0004035 name: acts upstream of, negative effect def: "c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term property_value: isDefinedBy http://purl.obolibrary.org/obo/ro.owl property_value: RO:0004050 RO:0002263 property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of,_negative_effect @@ -3645,29 +3711,6 @@ property_value: IAO:0000119 GROUP:OBI: xsd:s property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl is_metadata_tag: true -[Typedef] -id: has_part -name: has part -name: has_part -namespace: external -namespace: quality -def: "a core relation that holds between a whole and its part" [] -def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM] -comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. -xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -is_transitive: true -is_a: RO:0002131 ! overlaps - [Typedef] id: increased_in_magnitude_relative_to name: increased_in_magnitude_relative_to @@ -3680,38 +3723,6 @@ range: PATO:0000001 ! quality is_transitive: true is_a: different_in_magnitude_relative_to ! different_in_magnitude_relative_to -[Typedef] -id: part_of -name: part of -name: part_of -namespace: external -namespace: quality -def: "a core relation that holds between a part and its whole" [] -xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections -property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf -property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string -is_transitive: true -is_a: RO:0002131 ! overlaps -inverse_of: has_part ! has part - [Typedef] id: reciprocal_of name: reciprocal_of diff --git a/src/ontology/pco.owl b/src/ontology/pco.owl index fc88485..313a18f 100644 --- a/src/ontology/pco.owl +++ b/src/ontology/pco.owl @@ -17,7 +17,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland @@ -132,9 +132,9 @@ + definition definition - definition - textual definition + textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. @@ -161,9 +161,9 @@ We also have the outstanding issue of how to aim different definitions to differ PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + definition definition - definition - textual definition + textual definition @@ -227,8 +227,8 @@ We also have the outstanding issue of how to aim different definitions to differ Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w - Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source @@ -272,6 +272,7 @@ We also have the outstanding issue of how to aim different definitions to differ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. + term tracker item @@ -870,7 +871,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - has_obo_namespace @@ -919,7 +919,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - shorthand @@ -1031,7 +1030,6 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] - is part of @@ -1046,24 +1044,7 @@ EquivalentTo: xsd:integer[> 2151 , <= 2300] A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of - - - - - - - - BFO:0000050 - external - quality - part_of - part_of - - part of part of - part_of - - http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1072,13 +1053,11 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime @@ -1087,23 +1066,8 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part - BFO:0000051 - external - quality - has_part - has_part - We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. - - has part has part - has_part - - - - Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. - PATOC:CJM - @@ -1152,10 +1116,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. @@ -1176,10 +1136,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. @@ -1208,6 +1164,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in unfolds in unfolds_in + + + Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in @@ -1248,11 +1207,9 @@ Some currently missing phenomena that should be considered "about" are - - - - - has member of + + obsolete has member of + true @@ -1313,10 +1270,6 @@ Some currently missing phenomena that should be considered "about" are - - - - has participant this blood coagulation has participant this blood clot this investigation has participant this investigator @@ -1555,13 +1508,13 @@ Some currently missing phenomena that should be considered "about" are - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. - + This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. @@ -1603,78 +1556,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. - dos - 2017-05-24T09:30:46Z - - has regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. - dos - 2017-05-24T09:31:01Z - By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. - - has negative regulatory component activity - - - - - - - - - - A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. - dos - 2017-05-24T09:31:17Z - By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. - - has positive regulatory component activity - - - - - - - - - dos - 2017-05-24T09:44:33Z - A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. - - has component activity - - - - - - - - - - - w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - dos - 2017-05-24T09:49:21Z - - has component process - - - - @@ -1735,28 +1616,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - dos - 2017-09-22T14:14:36Z - This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. - - has effector activity - - - - - A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. - GOC:dos - - - - @@ -1805,56 +1664,16 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - - - - - - - - - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) + + overlaps - - - - - - - - true - - - - - - - - - - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. - The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - - - - has component - - @@ -1881,6 +1700,9 @@ Some currently missing phenomena that should be considered "about" are Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false + + + regulates @@ -1898,6 +1720,9 @@ Some currently missing phenomena that should be considered "about" are negatively regulates (process to process) + + + negatively regulates @@ -1920,6 +1745,9 @@ Some currently missing phenomena that should be considered "about" are positively regulates (process to process) + + + positively regulates @@ -1940,7 +1768,6 @@ Some currently missing phenomena that should be considered "about" are For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". - RO_0000053 some (RO_0000054 only ?Y) capable of @@ -1953,27 +1780,13 @@ Some currently missing phenomena that should be considered "about" are - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in - RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) capable of part of - - - - - - - - true - @@ -2001,11 +1814,13 @@ Some currently missing phenomena that should be considered "about" are - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes + + + has input @@ -2023,6 +1838,7 @@ Some currently missing phenomena that should be considered "about" are A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. + acts upstream of @@ -2041,6 +1857,7 @@ Some currently missing phenomena that should be considered "about" are A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects + acts upstream of or within @@ -2055,6 +1872,8 @@ Some currently missing phenomena that should be considered "about" are cjm + + holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect @@ -2107,14 +1926,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes @@ -2124,6 +1935,7 @@ Some currently missing phenomena that should be considered "about" are is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. + enables @@ -2146,25 +1958,12 @@ Some currently missing phenomena that should be considered "about" are - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false part of structure that is capable of - - - - - - - - true - @@ -2173,14 +1972,6 @@ Some currently missing phenomena that should be considered "about" are - - - - - - - - c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in @@ -2199,6 +1990,7 @@ Some currently missing phenomena that should be considered "about" are inverse of enables Chris Mungall + enabled by @@ -2358,6 +2150,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall + + causally upstream of @@ -2521,7 +2315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - GOC:cjm + GOC:cjm GOC:dos @@ -2664,25 +2458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in - - - - - - - - true - @@ -2817,6 +2598,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly regulates (processual) + + + directly regulates @@ -2828,10 +2612,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall @@ -2928,6 +2708,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly positively regulates (process to process) + + + directly positively regulates @@ -2943,6 +2726,9 @@ For example, A and B may be gene products and binding of B by A positively regul directly negatively regulates (process to process) + + + directly negatively regulates @@ -2953,10 +2739,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z @@ -2977,6 +2759,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:30Z + acts upstream of or within, positive effect @@ -2995,6 +2778,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:49:51Z + acts upstream of or within, negative effect @@ -3014,6 +2798,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:14Z + acts upstream of, positive effect @@ -3034,6 +2819,7 @@ For example, A and B may be gene products and binding of B by A positively regul cjm 2018-01-26T23:53:22Z + acts upstream of, negative effect @@ -3213,12 +2999,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3303,12 +3083,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -3380,12 +3154,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - ic @@ -3410,6 +3178,12 @@ For example, A and B may be gene products and binding of B by A positively regul independent continuant + + + + (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] + + @@ -3440,12 +3214,6 @@ For example, A and B may be gene products and binding of B by A positively regul (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] - - - - (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] - - @@ -3575,12 +3343,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - sdc SpecificallyDependentContinuant @@ -4145,22 +3907,25 @@ For example, A and B may be gene products and binding of B by A positively regul - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. + https://github.com/geneontology/go-ontology/issues/20191 interaction with another species interspecies interaction + interspecies interaction between organisms interspecies interaction with other organisms biological_process GO:0044419 + - interspecies interaction between organisms + biological process involved in interspecies interaction between organisms - Any process in which an organism has an effect on an organism of a different species. + Any process evolved to enable an interaction with an organism of a different species. GOC:cc @@ -4171,12 +3936,15 @@ For example, A and B may be gene products and binding of B by A positively regul Any process in which an organism has an effect on an organism of the same species. + https://github.com/geneontology/go-ontology/issues/20191 + intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 + - intraspecies interaction between organisms + biological process involved in intraspecies interaction between organisms @@ -6772,6 +6540,7 @@ No imports + @@ -7084,33 +6853,7 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - 2 - - - - - 1 - - - - - - - - - - - A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species @@ -7185,7 +6928,7 @@ Classes for population already exist in IDO ('organism population', I - + @@ -7489,7 +7232,6 @@ Classes for population already exist in IDO ('organism population', I - @@ -7732,61 +7474,196 @@ Classes for population already exist in IDO ('organism population', I - + - - - - - - 2 - - - - A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. - pair of interacting organisms + + + An organism that is part of a polyphyletic group of mostly photosynthetic Eukaryotes encompassing green plants excluding Embriophyta (land plants). Included organisms range from unicellular microalgae, such as Chlorella and diatoms to multicellular forms such as giant kelp. + + alga + algae + seaweed + alga excluding Cyanobacteria - + - - - - - - - 1 - - - - A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. - pair of interacting organisms of the same species + + + A community species diversity that is the mean species diversity at a site or within a specific habitat. + + + α-diversity + alpha diversity - + - - - - - - - - - - A population which is participating in a migration process. - migratory population + + + A community species diversity that is the ratio between regional and local species diversity. + + + true beta diversity + β-diversity + beta diversity - + - + + + A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. + + + γ-diversity + gamma diversity + + + + + + + + + TBD: add logical definition + + + The density of plants in an ecological community or population, often measured as the number of plants per area. + plant density + + + + + + + + + The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density + + + + + + + + + + The density of plants in a population or organisms (a single species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of a population + + + + + + + + + + The density of plants in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + plant density of an ecological community + + + + + + + + + + The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. + TBD: add logical definition + + + seedling density of a population + + + + + + + + + + The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. + TBD: add logical definition + + + seedling density of an ecological community + + + + + + + + + + + + + + 2 + + + + + + + A collection of organisms that consists of exactly two organism, viruses, or viroids that are interacting with each other. + pair of interacting organisms + + + + + + + + + + + A pair of interacting organisms that consists of exactly two organism, viruses, or viroids of the same species that are interacting with each other. + pair of interacting organisms of the same species + + + + + + + + + + + + + + + + A population which is participating in a migration process. + migratory population + + + + + + + A population process during which a population moves from one area to another. @@ -7883,9 +7760,15 @@ Classes for population already exist in IDO ('organism population', I - - Obsolete Class - + + + + + + + + + @@ -8277,12 +8160,6 @@ Classes for population already exist in IDO ('organism population', I /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - @@ -8292,15 +8169,6 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - @@ -8313,85 +8181,15 @@ Classes for population already exist in IDO ('organism population', I - - - - - - - - - - - - - - - - + - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z @@ -8464,18 +8262,16 @@ Classes for population already exist in IDO ('organism population', I - GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), -e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' - enabling an MF enables its parts - - - + + + + @@ -8483,10 +8279,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + @@ -8495,12 +8290,25 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - + + + + + + + + + + + + + + @@ -8513,9 +8321,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -8523,18 +8331,17 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP + 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). - - - + + + + @@ -8543,25 +8350,12 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + - - - - - - - - - - - - - - + @@ -8571,17 +8365,29 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - + + + + + + + + + + + + + + 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). @@ -8589,79 +8395,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" - - - - - - - - - - + + + @@ -8670,364 +8406,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - - - - - - - - - - - - - - - - If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. - inferring direct reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct neg reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - inferring direct positive reg edge from input to regulatory subfunction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - effector input is compound function input - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Input of effector is input of its parent MF - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly regulates X, its parent MF directly regulates X - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - if effector directly positively regulates X, its parent MF directly positively regulates X - - - - - - - - - - - - - - - - - - - - - + + + @@ -9040,28 +8421,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - - - if effector directly negatively regulates X, its parent MF directly negatively regulates X - - - - - - - - - - + + + @@ -9069,30 +8431,15 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - + + + - - - - - - - - - - - - - - diff --git a/src/ontology/reports/nolabels-violation.csv b/src/ontology/reports/nolabels-violation.csv new file mode 100644 index 0000000..f07f4a9 --- /dev/null +++ b/src/ontology/reports/nolabels-violation.csv @@ -0,0 +1,2 @@ +cls +http://purl.obolibrary.org/obo/GO_0051704 diff --git a/src/ontology/reports/pco-edit.owl-obo-report.tsv b/src/ontology/reports/pco-edit.owl-obo-report.tsv index 02983a2..0d2c93a 100644 --- a/src/ontology/reports/pco-edit.owl-obo-report.tsv +++ b/src/ontology/reports/pco-edit.owl-obo-report.tsv @@ -1,17 +1,18 @@ Level Rule Name Subject Property Value -ERROR missing_label BFO:0000017 rdfs:label -ERROR missing_label ECOCORE:00000045 rdfs:label -ERROR missing_label GO:0051704 rdfs:label -ERROR missing_label IAO:0000030 rdfs:label -ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en -ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en -WARN missing_definition BFO:0000017 IAO:0000115 -WARN missing_definition ECOCORE:00000045 IAO:0000115 -WARN missing_definition GO:0051704 IAO:0000115 -WARN missing_definition IAO:0000030 IAO:0000115 -WARN missing_definition PCO:0000049 IAO:0000115 -WARN missing_definition PCO:0000055 IAO:0000115 -INFO missing_superclass PCO:0000003 rdfs:subClassOf -INFO missing_superclass PCO:0000004 rdfs:subClassOf -INFO missing_superclass PCO:0000050 rdfs:subClassOf -INFO missing_superclass PCO:0000052 rdfs:subClassOf +ERROR missing_label BFO:0000017 rdfs:label +ERROR missing_label ECOCORE:00000045 rdfs:label +ERROR missing_label GO:0051704 rdfs:label +ERROR missing_label IAO:0000030 rdfs:label +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as members every organism of given species and no organisms of any other species.@en +ERROR multiple_definitions PCO:0000017 IAO:0000115 A collection of organisms that has as parts every organism of a species and no organisms of any other species.@en +WARN missing_definition BFO:0000017 IAO:0000115 +WARN missing_definition ECOCORE:00000045 IAO:0000115 +WARN missing_definition GO:0051704 IAO:0000115 +WARN missing_definition IAO:0000030 IAO:0000115 +WARN missing_definition PCO:0000049 IAO:0000115 +WARN missing_definition PCO:0000077 IAO:0000115 +INFO missing_superclass PCO:0000003 rdfs:subClassOf +INFO missing_superclass PCO:0000004 rdfs:subClassOf +INFO missing_superclass PCO:0000050 rdfs:subClassOf +INFO missing_superclass PCO:0000052 rdfs:subClassOf +INFO missing_superclass PCO:0001000 rdfs:subClassOf